diff --git a/ArraysAmbiguousSNPMiscallingMar2019/README.md b/ArraysAmbiguousSNPMiscallingMar2019/README.md index 4489c80..4082af1 100755 --- a/ArraysAmbiguousSNPMiscallingMar2019/README.md +++ b/ArraysAmbiguousSNPMiscallingMar2019/README.md @@ -44,5 +44,6 @@ For example (from within the ArraysAmbiguousSNPMiscallingMar2019 directory): After filtering, the script runs a sanity check to see that the correct number of sites have been filtered. If the script ran successfully, a message in the end should tell you so. The script attempts to clean up after itself but leaves log files around. +## Assessing and Fixing Miscalling Bugs in PLINK files - +The subdirectory `allele_flip` provides tools for assessing whether your PLINK format genotyping data is affected by the strand ambiguous bug, and for fixing the bug through flipping DNA strand. Please refer to `allele_flip/README.md` for details. diff --git a/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/1000_Genomes_AF/Broad_GWAS_supplemental_15061359_A1.1.3.1000_Genomes_AF.txt b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/1000_Genomes_AF/Broad_GWAS_supplemental_15061359_A1.1.3.1000_Genomes_AF.txt new file mode 100644 index 0000000..f129950 --- /dev/null +++ b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/1000_Genomes_AF/Broad_GWAS_supplemental_15061359_A1.1.3.1000_Genomes_AF.txt @@ -0,0 +1,194 @@ +chr position ID A1 A2 af_eur af_eas af_afr +1 2283313 rs2843130 C G 0.165 0.2312 0.025 +1 12837634 rs848578 T A 0.8012 0.7192 0.3729 +1 28203653 rs11247703 C G 0.2893 0.3472 0.2065 +1 36934805 rs3917991 C G 0.0189 0.0 0.1732 +1 47266422 rs837398 T A 0.7932 0.6935 0.4493 +1 57892924 rs7523104 A T 0.1879 0.0327 0.3979 +1 67266756 rs549148 T A 0.83 0.9901 0.7821 +1 67793171 rs10489626 C G 0.162 0.0585 0.2065 +1 71357687 rs17131479 C G 0.0388 0.2073 0.2428 +1 84864256 rs3738573 G C 0.334 0.4038 0.1755 +1 88350912 rs2503243 G C 0.3897 0.3621 0.8676 +1 93720070 rs12030843 C G 0.1511 0.3175 0.1974 +1 97735667 rs1520668 G C 0.0089 0.1647 0.1974 +1 99418647 rs309087 G C 0.1789 0.2351 0.2738 +1 109633256 rs521734 C G 0.4026 0.4831 0.9501 +1 117299472 rs3136701 G C 0.3678 0.4812 0.6566 +1 154239283 rs1212352 T A 0.5994 0.5655 0.8676 +1 157805650 rs11537583 A T 0.007 0.1736 0.1619 +1 169482115 rs9332678 A T 0.0239 0.6062 0.1558 +1 169658509 rs4987389 A T 0.1859 0.3829 0.4864 +1 179876988 rs609521 C G 0.6093 0.7778 0.3041 +1 182026813 rs12568050 G C 0.1471 0.2837 0.09 +1 204132638 rs6693954 T A 0.2555 0.1915 0.5008 +1 207007641 rs2243158 C G 0.9155 0.7956 0.8366 +1 213011812 rs7524203 G C 0.5507 0.5377 0.2345 +1 228520973 rs369909 C G 0.4205 0.249 0.4183 +2 54808845 rs12713268 C G 0.2197 0.1062 0.7088 +2 71160222 rs2234500 C G 0.1093 0.2262 0.2118 +2 80144920 rs2916519 A T 0.5547 0.7768 0.7231 +2 88913273 rs867529 G C 0.2982 0.4851 0.0166 +2 101898412 rs13151 G C 0.8738 1.0 0.6278 +2 108994808 rs1402467 C G 0.2634 0.1081 0.8752 +2 128388862 rs13025959 G C 0.2018 0.1349 0.0499 +2 165843619 rs1993308 C G 0.9493 0.7619 0.5855 +2 182625313 rs2037799 T A 0.0278 0.2381 0.4349 +2 185800905 rs12476147 A T 0.6193 0.8373 0.438 +2 200613782 rs12693898 G C 0.9105 0.8452 0.4334 +2 215645464 rs2229571 C G 0.6412 0.3413 0.379 +2 219658170 rs12987009 A T 0.4284 0.0565 0.2216 +2 220421417 rs1983210 C G 0.7366 0.7163 0.6036 +2 225511361 rs2047136 A T 0.6302 0.8353 0.9478 +2 228855866 rs16824283 G C 0.3022 0.2282 0.0303 +3 24805012 rs4858649 T A 0.6431 0.8046 0.7088 +3 50210289 rs1005678 C G 0.4105 0.6567 0.5817 +3 88514766 rs11713321 T A 0.7674 0.7014 0.1868 +3 111286375 rs2276872 G C 0.003 0.1558 0.0696 +3 133700071 rs5013525 C G 0.3907 0.25 0.2095 +3 150257082 rs10935807 C G 0.3757 0.4008 0.1967 +3 155196730 rs6798100 C G 0.2495 0.4196 0.8865 +3 170717521 rs11920090 T A 0.1352 0.0169 0.3744 +3 183761664 rs7430671 G C 0.5288 0.8988 0.3578 +4 9995182 rs3775948 G C 0.7545 0.5813 0.6634 +4 16641382 rs1972463 G C 0.7167 0.5724 0.5847 +4 38333458 rs13101978 T A 0.5934 0.0278 0.292 +4 46027834 rs10014198 G C 0.4284 0.3284 0.6808 +4 55446565 rs17084491 G C 0.004 0.0 0.3782 +4 70600199 rs13133166 C G 0.4771 0.7173 0.5598 +4 88295008 rs10222732 C G 0.2525 0.0952 0.2209 +4 100274157 rs4147541 G C 0.2594 0.7649 0.4992 +4 187210247 rs1062547 A T 0.3887 0.1647 0.5832 +5 9332281 rs7702187 T A 0.834 0.7321 0.3457 +5 10654769 rs3822410 C G 0.3121 0.2599 0.416 +5 40955561 rs1063499 G C 0.5855 0.5218 0.3048 +5 68419054 rs164572 A T 0.4225 0.5397 0.2519 +5 74400386 rs961098 G C 0.1819 0.1925 0.1089 +5 115156261 rs10059199 C G 0.002 0.0 0.3585 +5 150402490 rs3792796 G C 0.6372 0.3472 0.1679 +6 6287216 rs1993554 G C 0.1093 0.2431 0.1362 +6 24496314 rs2010190 G C 0.9155 0.5853 0.7595 +6 28511164 rs454182 G C 0.2634 0.5476 0.7383 +6 28846724 rs209151 G C 0.2913 0.5317 0.3048 +6 29479533 rs1010408 T A 0.4165 0.2946 0.5567 +6 29662374 rs3094736 T A 0.5229 0.5734 0.6195 +6 29831571 rs1611737 C G 0.4046 0.4593 0.472 +6 29868064 rs3128994 G C 0.7376 0.5913 0.7262 +6 30192467 rs9261578 C G 0.1799 0.2093 0.2519 +6 30387890 rs1264540 G C 0.4423 0.7024 0.1989 +6 30496816 rs2534823 C G 0.673 0.621 0.77 +6 30999902 rs4713422 G C 0.4036 0.5268 0.4085 +6 31080828 rs2233967 C G 0.1571 0.3175 0.0492 +6 31118565 rs130078 C G 0.7813 0.6756 0.7292 +6 31335806 rs9266399 A T 0.2147 0.3909 0.2398 +6 31345486 rs7775117 T A 0.2416 0.3026 0.351 +6 32054212 rs2239688 C G 0.003 0.2232 0.0008 +6 32193698 rs9267845 A T 0.4264 0.6706 0.5371 +6 32561334 rs35265698 C G 0.159 0.12 0.0356 +6 32581582 rs9271300 C G 0.5497 0.4425 0.5893 +6 53066595 rs9474433 C G 0.1262 0.001 0.3018 +6 74073531 rs561930 C G 0.5716 0.5397 0.3064 +6 74234043 rs9446917 T A 0.7376 0.7252 0.7769 +6 98980113 rs211221 C G 0.2575 0.1895 0.2867 +6 161115245 rs7772437 A T 0.4861 0.1815 0.4251 +7 2458129 rs10245377 G C 0.1769 0.1558 0.3775 +7 44809276 rs1065647 G C 0.4692 0.746 0.6513 +7 64349871 rs884103 T A 0.9125 0.7758 0.8056 +7 75822876 rs10245531 C G 0.7495 0.6577 0.9879 +7 94955221 rs705382 C G 0.6501 0.5466 0.2405 +7 95020061 rs10487131 A T 0.2346 0.5962 0.0393 +7 95050946 rs7801803 T A 0.5 0.8254 0.7095 +7 133988313 rs2598291 C G 0.4652 0.2708 0.6044 +7 140198159 rs7781853 G C 0.4264 0.3829 0.3011 +7 150726920 rs6944935 C G 0.2515 0.2788 0.329 +7 154868879 rs1440451 G C 0.995 1.0 0.4728 +7 157985149 rs3800855 C G 0.169 0.1944 0.3752 +8 6302183 rs930557 G C 0.7982 0.7639 0.2458 +8 11617240 rs12458 A T 0.3211 0.5546 0.3933 +8 12870160 rs2460338 G C 0.2783 0.62 0.2171 +8 28183219 rs2614091 G C 0.4364 0.1399 0.0514 +8 42414226 rs12677427 T A 0.5835 0.5079 0.4266 +8 107494071 rs2167801 A T 0.7276 0.3452 0.6702 +8 121081153 rs2875931 C G 0.3807 0.1131 0.4289 +8 137402605 rs7812449 A T 0.001 0.0 0.1891 +9 94682964 rs10116326 C G 0.1044 0.4147 0.7224 +9 95293641 rs10118939 C G 0.2932 0.0893 0.7526 +9 107604394 rs3824479 T A 0.0636 0.4177 0.0106 +9 107633623 rs1929842 G C 0.2117 0.2421 0.7148 +9 111651620 rs3204145 A T 0.172 0.2937 0.3245 +9 136412013 rs2073873 G C 0.1531 0.1438 0.0129 +9 137287629 rs11103473 T A 0.6521 0.7292 0.2012 +10 15115719 rs4748140 C G 0.4453 0.5873 0.4334 +10 22844099 rs4747442 C G 0.6103 0.5516 0.2073 +10 89463460 rs7923151 G C 0.4026 0.4315 0.7738 +10 91468925 rs3758383 C G 0.2416 0.3621 0.0492 +10 96575069 rs1853205 C G 0.1451 0.3125 0.2126 +10 96602398 rs28399513 T A 0.1451 0.3125 0.1702 +10 121217061 rs1999628 T A 0.0895 0.2996 0.0023 +11 1702055 rs4752781 A T 0.4294 0.8254 0.0582 +11 3865786 rs1026231 C G 0.5268 0.4077 0.4402 +11 4907216 rs10500633 T A 0.2247 0.0258 0.1346 +11 12255471 rs11022257 C G 0.2903 0.5218 0.1505 +11 46744925 rs2070852 G C 0.7078 0.3026 0.1263 +11 65420760 rs10896027 C G 0.3469 0.256 0.059 +11 76912636 rs2276288 A T 0.5656 0.4524 0.7254 +11 88380551 rs7396702 C G 0.8847 0.8155 0.2103 +11 92886648 rs10830989 C G 0.66 0.7887 0.4425 +11 95853028 rs11021436 C G 0.2962 0.6677 0.351 +11 107663103 rs516091 C G 0.4791 0.1468 0.3843 +11 121452651 rs11218350 T A 0.2396 0.5556 0.0825 +12 10313448 rs11053646 C G 0.0835 0.1746 0.2209 +12 27850113 rs12819160 A T 0.175 0.0506 0.0068 +12 32135186 rs3759302 T A 0.1869 0.121 0.0756 +12 40713901 rs11564148 T A 0.3171 0.3373 0.174 +13 37132985 rs12323063 T A 0.4066 0.1756 0.6581 +13 40229957 rs3812883 T A 0.3767 0.4573 0.5015 +13 69199984 rs287398 T A 0.3539 0.3631 0.4319 +13 73256676 rs9543067 A T 0.327 0.4603 0.3616 +14 23612489 rs2273394 C G 0.7614 0.8393 0.8411 +14 47466177 rs9323124 T A 0.2396 0.0288 0.1899 +14 50049252 rs12436916 T A 0.2028 0.002 0.2005 +14 74551970 rs2239557 G C 0.3449 0.7946 0.4849 +15 25154880 rs4906695 G C 0.162 0.3423 0.0408 +15 41991315 rs2178004 A T 0.835 0.8909 0.5083 +15 45567437 rs1706766 A T 0.0 0.0 0.2383 +15 45571209 rs7166580 C G 0.6372 0.1181 0.4349 +15 58674695 rs4775041 G C 0.2972 0.1944 0.0862 +15 61755995 rs8034331 C G 0.7147 0.374 0.2791 +15 76236837 rs1874953 G C 0.502 0.6379 0.2663 +15 90213229 rs6496589 G C 0.9861 0.7619 0.9788 +16 2897411 rs11076863 G C 0.2386 0.1359 0.3003 +16 16236004 rs212090 T A 0.4553 0.1786 0.1263 +16 17855194 rs9924528 A T 0.1272 0.2679 0.2685 +17 7342148 rs4151120 T A 0.3489 0.001 0.3396 +17 7849087 rs4462665 C G 0.4493 0.8016 0.5424 +17 20456522 rs9908604 G C 0.7068 0.623 0.7012 +17 29297910 rs7221473 C G 0.0119 0.001 0.798 +17 33875262 rs8073060 T A 0.3201 0.1815 0.4766 +17 44059010 rs17651507 A T 0.2336 0.1706 0.0113 +18 10095556 rs1941059 G C 0.2833 0.2054 0.1619 +18 33828980 rs567458 C G 0.5477 0.3125 0.7557 +18 44475220 rs10853545 A T 0.5666 0.3452 0.6899 +19 582927 rs8259 T A 0.3032 0.6855 0.556 +19 5793704 rs2446195 C G 0.1938 0.5476 0.7943 +19 6702157 rs428453 C G 0.6272 0.8512 0.7103 +19 10772685 rs10419865 G C 0.5924 0.6438 0.6959 +19 15779672 rs10418069 T A 0.2177 0.4732 0.6407 +19 16025919 rs12977516 G C 0.4662 0.2222 0.2663 +19 16890243 rs773930 C G 0.0427 0.0 0.5817 +19 18180413 rs401502 C G 0.3121 0.376 0.1747 +19 36975448 rs2967456 C G 0.662 0.2589 0.6165 +19 44471209 rs365745 T A 0.8539 0.8452 0.4841 +19 45882962 rs6966 T A 0.164 0.4425 0.6982 +19 47856140 rs1064202 G C 0.1213 0.4464 0.5522 +19 48374551 rs296365 C G 0.7376 0.7827 0.3805 +19 48608598 rs2307279 C G 0.0497 0.2698 0.5779 +19 52115645 rs3829655 G C 0.4225 0.5794 0.3275 +19 53577419 rs8105668 G C 0.8082 0.6032 0.9281 +20 168728 rs4813043 T A 0.6093 0.4554 0.7867 +20 23318014 rs1891687 T A 0.004 0.0873 0.407 +20 44642406 rs2250889 G C 0.9543 0.7718 0.8283 +20 45186748 rs12617 T A 0.6859 0.9454 0.8502 +22 19948863 rs165656 G C 0.504 0.2688 0.4175 +22 29887186 rs710195 G C 0.6272 0.873 0.7564 +22 45255637 rs6007344 G C 0.1899 0.4048 0.3207 diff --git a/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/1000_Genomes_AF/GSA-24v1-0_A1.1.3.1000_Genomes_AF.txt b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/1000_Genomes_AF/GSA-24v1-0_A1.1.3.1000_Genomes_AF.txt new file mode 100644 index 0000000..1c57bf5 --- /dev/null +++ b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/1000_Genomes_AF/GSA-24v1-0_A1.1.3.1000_Genomes_AF.txt @@ -0,0 +1,2350 @@ +chr position ID A1 A2 af_eur af_eas af_afr +1 979748 rs113288277 A T 0.0467 0.0079 0.0008 +1 980824 seq-rs112039851 G C 0.003 0.0268 0.0726 +1 1267291 rs76584377 G C 0.0 0.0 0.0144 +1 1650885 rs201091435 T A 0.0 0.0 0.0015 +1 1848197 rs74773083 G C 0.0 0.0 0.0333 +1 5947504 rs201527181 G C 0.0 0.0 0.0038 +1 5947525 rs200821373 T A 0.0 0.0 0.0008 +1 6279370 rs846111 G C 0.2604 0.1756 0.0227 +1 9307230 rs12032814 T A 0.2435 0.4067 0.2088 +1 9809604 rs186712596 C G 0.0 0.0 0.0 +1 9815316 rs199722695 A T 0.001 0.0 0.0 +1 11853994 rs116620395 C G 0.001 0.0 0.0008 +1 14068545 rs188038052 C G 0.0 0.003 0.0 +1 19546189 rs201239769 C G 0.0 0.002 0.0 +1 19635068 rs141532320 G C 0.001 0.0 0.0 +1 20227723 rs4654925 G C 0.4443 0.2331 0.4289 +1 20931828 rs818194 A T 0.7922 0.8175 0.5204 +1 21546474 rs186453862 G C 0.0 0.005 0.0 +1 22170652 rs139838884 C G 0.0 0.0 0.003 +1 22191473 rs138460117 A T 0.002 0.0 0.0 +1 22816686 rs201681716 A T 0.0 0.0 0.0008 +1 22987724 rs147260497 A T 0.0 0.0 0.0023 +1 23357092 rs201256608 A T 0.0 0.001 0.0 +1 23536891 rs1738475 C G 0.4175 0.4504 0.6399 +1 24083609 rs145432831 G C 0.0 0.0 0.0008 +1 25719599 1:25719599-T-A T A 0.5527 0.2272 0.8699 +1 26135083 rs199742668 G C 0.0 0.001 0.0113 +1 26392828 rs41284325 C G 0.001 0.0 0.0 +1 27190208 rs202094692 C G 0.0 0.0 0.0 +1 27697425 rs138940198 G C 0.0 0.0 0.0045 +1 29190390 rs204076 T A 0.6799 0.9038 0.8464 +1 31347375 rs141616997 C G 0.0 0.001 0.0 +1 35369014 rs10493064 T A 0.1541 0.4494 0.1346 +1 36934805 rs3917991 C G 0.0189 0.0 0.1732 +1 38281179 rs200294506 C G 0.0 0.0 0.0 +1 38353098 rs190711865 A T 0.0 0.0 0.003 +1 38409317 rs201533855 A T 0.002 0.0 0.0 +1 39833826 rs145646053 A T 0.0 0.0079 0.0 +1 39895727 rs145430083 A T 0.001 0.0 0.0 +1 40539817 rs72937434 C G 0.0 0.0 0.0946 +1 40557070 rs137852695 T A 0.003 0.0 0.0 +1 40954877 rs34752670 G C 0.0 0.0 0.0363 +1 40961133 rs144613252 A T 0.004 0.0 0.0 +1 43218037 rs201977455 C G 0.0 0.0 0.0 +1 43299192 JHU_1.43299191 A T 0.0089 0.0 0.034 +1 43308702 exm2251756 A T 0.0 0.0 0.0008 +1 43651024 rs74857529 C G 0.0089 0.0 0.0 +1 44121557 rs2274465 C G 0.3241 0.2302 0.0877 +1 44363909 rs201834329 A T 0.0 0.0 0.0 +1 44474217 rs192630770 T A 0.0 0.0089 0.0 +1 45228236 rs151202038 A T 0.001 0.0 0.0 +1 46080809 rs139279656 C G 0.005 0.0 0.0 +1 46081138 rs189842615 A T 0.0 0.0 0.0 +1 47799639 rs7543016 G C 0.4602 0.5843 0.8245 +1 51477643 rs13376700 T A 0.4354 0.2212 0.6762 +1 53666438 rs201966320 C G 0.001 0.0 0.0 +1 53679110 rs201913567 C G 0.0 0.001 0.0 +1 55223744 rs35201073 G C 0.001 0.0 0.0 +1 57224387 rs142698557 A T 0.0 0.0069 0.0 +1 57411642 rs146176997 C G 0.0 0.0 0.0053 +1 62550238 rs201822318 C G 0.0 0.003 0.0 +1 63918318 GSA-rs9436673 T A 0.4394 0.4683 0.5098 +1 65095158 rs182323946 G C 0.002 0.0 0.0 +1 65145377 rs199862686 A T 0.0 0.0 0.0 +1 67705933 rs201752419 A T 0.0 0.001 0.0 +1 67861690 rs147267211 C G 0.001 0.0 0.0 +1 74991402 rs1514177 C G 0.5716 0.2272 0.3585 +1 78383669 rs199720912 G C 0.001 0.0 0.0 +1 78401664 rs35366555 G C 0.0 0.0 0.0091 +1 86304311 rs190550059 C G 0.0 0.0 0.0 +1 86515845 rs117013561 G C 0.0 0.004 0.0 +1 89735081 rs61732483 T A 0.0 0.0 0.1097 +1 92187536 rs11466592 A T 0.0 0.0 0.0061 +1 92737184 rs145762716 G C 0.0 0.0079 0.0 +1 93720070 rs12030843 C G 0.1511 0.3175 0.1974 +1 94463425 rs61748521 G C 0.001 0.0 0.0 +1 97547947 rs67376798 T A 0.007 0.0 0.0008 +1 98045449 rs75017182 G C 0.0239 0.0 0.0008 +1 98058848 rs190577302 G C 0.0 0.0 0.0008 +1 98552832 rs1198588 A T 0.7704 0.9296 0.702 +1 100573410 rs199910652 C G 0.0 0.001 0.0 +1 109351463 rs201321358 A T 0.001 0.0 0.0 +1 109795742 rs115856488 T A 0.006 0.0 0.0 +1 109812652 rs201787934 G C 0.0 0.002 0.0 +1 111861142 rs181434663 A T 0.0 0.0 0.0 +1 111861741 rs147847412 G C 0.0 0.0 0.0008 +1 112302035 rs141366359 C G 0.0 0.0 0.0061 +1 112303149 rs200556382 C G 0.0 0.001 0.0 +1 113616048 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a/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/1000_Genomes_AF/GSAMD-24v1-0_20011747_A1.1.3.1000_Genomes_AF.txt b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/1000_Genomes_AF/GSAMD-24v1-0_20011747_A1.1.3.1000_Genomes_AF.txt new file mode 100644 index 0000000..744f0c2 --- /dev/null +++ b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/1000_Genomes_AF/GSAMD-24v1-0_20011747_A1.1.3.1000_Genomes_AF.txt @@ -0,0 +1,2448 @@ +chr position ID A1 A2 af_eur af_eas af_afr +1 979748 rs113288277 A T 0.0467 0.0079 0.0008 +1 980824 seq-rs112039851 G C 0.003 0.0268 0.0726 +1 1267291 rs76584377 G C 0.0 0.0 0.0144 +1 1650885 rs201091435 T A 0.0 0.0 0.0015 +1 1848197 rs74773083 G C 0.0 0.0 0.0333 +1 3807344 seq-rs143229412 C G 0.0 0.0 0.0061 +1 5947504 rs201527181 G C 0.0 0.0 0.0038 +1 5947525 rs200821373 T A 0.0 0.0 0.0008 +1 6279370 rs846111 G C 0.2604 0.1756 0.0227 +1 9307230 rs12032814 T A 0.2435 0.4067 0.2088 +1 9809604 rs186712596 C G 0.0 0.0 0.0 +1 9815316 rs199722695 A T 0.001 0.0 0.0 +1 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rs199510610 C G 0.0 0.0 0.0008 +22 19920359 rs9606186 C G 0.5865 0.7232 0.6112 +22 21075586 seq-rs144899078 G C 0.0 0.0 0.0015 +22 24843594 rs4822492 C G 0.5865 0.4702 0.2042 +22 24999104 rs2073398 C G 0.3668 0.375 0.205 +22 25599770 rs200457939 T A 0.0 0.0 0.0 +22 26157068 rs61734946 C G 0.1839 0.002 0.0129 +22 29196757 rs2269577 G C 0.2972 0.6528 0.5764 +22 30592487 rs713875 C G 0.5477 0.6696 0.3343 +22 30659996 seq-rs115760188.1 C G 0.0 0.001 0.0008 +22 32211147 rs193042481 C G 0.001 0.0 0.0 +22 35799487 rs12170872 G C 0.0 0.0 0.0045 +22 36688226 rs200616409 C G 0.0 0.001 0.0 +22 37632770 rs13058338 T A 0.2644 0.0694 0.0855 +22 38130827 rs183455182 A T 0.0 0.0089 0.0 +22 38165091 rs200313246 A T 0.0 0.0 0.0015 +22 38371396 rs139887 G C 0.6332 0.7371 0.4803 +22 38455469 rs713729 T A 0.2763 0.1915 0.0204 +22 38683637 rs135745 G C 0.5249 0.1478 0.3956 +22 39739638 rs137686 C G 0.7396 0.87 0.8313 +22 39747671 rs909685 T A 0.3012 0.7867 0.4788 +22 40816889 rs200555648 C G 0.004 0.0 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0.1899 0.4048 0.3207 +22 45258242 exm1616648 G C 0.0 0.0 0.0015 +22 45258373 exm1616670 G C 0.0348 0.0 0.0015 +22 45683116 exm1616988 A T 0.0 0.0 0.0522 +22 45691446 exm1617030 T A 0.0 0.0 0.0015 +22 45740462 exm1617131 C G 0.0 0.0288 0.0 +22 45795041 exm1617218 A T 0.001 0.0 0.0 +22 46327122 exm1617624 G C 0.0 0.0 0.0015 +22 46652516 exm1617823 T A 0.002 0.001 0.0 +22 46655779 exm1617965 G C 0.1233 0.001 0.0802 +22 46655919 exm1617966 T A 0.001 0.0 0.0 +22 46658471 exm1618077 G C 0.0 0.0 0.0 +22 46724650 exm2015831 G C 0.0 0.003 0.0 +22 46725974 exm1618350 C G 0.0 0.0099 0.0 +22 46746276 exm2015856 C G 0.0 0.0 0.0 +22 46760481 exm1618494 C G 0.2455 0.005 0.5492 +22 46762970 exm1618550 G C 0.001 0.0 0.0 +22 46932032 exm1619080 T A 0.002 0.0 0.0 +22 47106996 exm1619303 C G 0.002 0.0 0.0008 +22 47189678 exm1619369 C G 0.0199 0.0 0.0008 +22 50169346 exm2255261 G C 0.0 0.0 0.0076 +22 50217649 exm1619708 C G 0.0 0.0 0.0151 +22 50278356 exm1619786 C G 0.0 0.0 0.0015 +22 50313441 exm1620056 G 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0.2569 0.3177 +1 5327683 kgp11593089 G C 0.0636 0.002 0.0038 +1 5336806 kgp6919325 A T 0.2296 0.0625 0.0098 +1 5475598 kgp4238958 C G 0.1571 0.2133 0.1755 +1 5514373 kgp4768667 C G 0.4006 0.1121 0.239 +1 5640332 kgp1667199 C G 0.3181 0.6696 0.3026 +1 5676653 kgp10663388 G C 0.1829 0.0685 0.0719 +1 5719422 kgp2925954 C G 0.3171 0.5248 0.3321 +1 5868319 kgp9477054 T A 0.0139 0.0 0.0023 +1 5913428 kgp1806749 C G 0.0964 0.0615 0.0703 +1 5961596 kgp2068221 T A 0.0119 0.0 0.0 +1 6067640 kgp6213492 C G 0.8429 0.7034 0.7511 +1 6148922 kgp8553112 G C 0.1044 0.3393 0.118 +1 6170699 kgp9704502 C G 0.0964 0.1974 0.143 +1 6266994 kgp10460375 G C 0.0557 0.0972 0.4357 +1 6291314 kgp15615211 C G 0.007 0.0 0.1694 +1 6392346 kgp15162659 T A 0.0 0.0 0.0998 +1 6572271 kgp1061095 C G 0.2396 0.6022 0.3343 +1 6573038 kgp2275568 C G 0.6839 0.7282 0.2821 +1 6686022 kgp5073873 G C 0.0696 0.001 0.0053 +1 6720932 kgp6455249 C G 0.9254 0.5734 0.8782 +1 6791386 kgp10860467 T A 0.3459 0.5188 0.5825 +1 7092429 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kgp22769403 T A 0.0875 0.2679 0.0461 diff --git a/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/1000_Genomes_AF/HumanOmniExpress-12v1_H.1.3.1000_Genomes_AF.txt b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/1000_Genomes_AF/HumanOmniExpress-12v1_H.1.3.1000_Genomes_AF.txt new file mode 100644 index 0000000..59d1593 --- /dev/null +++ b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/1000_Genomes_AF/HumanOmniExpress-12v1_H.1.3.1000_Genomes_AF.txt @@ -0,0 +1,1220 @@ +chr position ID A1 A2 af_eur af_eas af_afr +1 1346905 rs1240719 T A 0.0964 0.1111 0.7322 +1 1439671 rs12021879 C G 0.007 0.3611 0.3616 +1 2283313 rs2843130 C G 0.165 0.2312 0.025 +1 11733866 rs28924120 G C 0.0 0.0 0.0008 +1 12339619 rs4845898 A T 0.2356 0.1964 0.0151 +1 12837634 rs848578 T A 0.8012 0.7192 0.3729 +1 24447468 rs3795299 G C 0.3996 0.7252 0.2874 +1 24695151 rs7537875 T A 0.3628 0.4177 0.3873 +1 25687308 rs8876 C G 0.0417 0.0 0.0 +1 27239920 rs6659176 C G 0.0746 0.006 0.0552 +1 27682530 rs17162549 C G 0.0547 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0.4743 +19 5793704 rs2446195 C G 0.1938 0.5476 0.7943 +19 6702157 rs428453 C G 0.6272 0.8512 0.7103 +19 6718387 rs2230199 G C 0.2207 0.003 0.0333 +19 7573098 rs475923 T A 0.3628 0.1746 0.295 +19 10444603 rs2230399 C G 0.0755 0.003 0.2383 +19 10621208 rs10409101 G C 0.1302 0.0169 0.1641 +19 10772685 rs10419865 G C 0.5924 0.6438 0.6959 +19 15755392 rs2077080 G C 0.3499 0.6954 0.6611 +19 15762678 rs2683035 A T 0.2694 0.1558 0.1082 +19 15762938 rs2683037 T A 0.2694 0.1567 0.1067 +19 15763798 rs2683039 G C 0.2694 0.1558 0.1067 +19 15769379 rs4646515 G C 0.3569 0.6627 0.677 +19 15769992 rs2460817 A T 0.9702 1.0 1.0 +19 15772564 rs4358060 T A 0.4175 0.5169 0.5197 +19 15774661 rs7253222 A T 0.4165 0.5169 0.6445 +19 15779672 rs10418069 T A 0.2177 0.4732 0.6407 +19 15918802 rs4808383 C G 0.1779 0.12 0.1331 +19 15994478 rs2886296 A T 0.9414 1.0 0.9977 +19 15996349 rs3093166 A T 0.6441 0.4375 0.7277 +19 16025919 rs12977516 G C 0.4662 0.2222 0.2663 +19 16890243 rs773930 C G 0.0427 0.0 0.5817 +19 16926067 rs11671361 A T 0.2515 0.0933 0.056 +19 18180413 rs401502 C G 0.3121 0.376 0.1747 +19 18377496 rs8104533 C G 0.4294 0.5516 0.6929 +19 18497141 rs1059369 T A 0.2475 0.4236 0.1762 +19 19740729 rs880090 C G 0.7584 0.7629 0.5628 +19 33470806 rs8112607 G C 0.1332 0.002 0.0772 +19 34177652 rs10415177 C G 0.1889 0.0188 0.059 +19 34260989 rs285694 C G 0.5179 0.2986 0.7882 +19 36975448 rs2967456 C G 0.662 0.2589 0.6165 +19 38376485 rs10408510 T A 0.7485 0.8998 0.9766 +19 39400175 rs10775533 C G 0.66 0.9742 0.4637 +19 39888390 rs1057745 G C 0.0885 0.0942 0.0877 +19 39915758 rs31728 C G 0.5338 0.6002 0.677 +19 41624416 rs11670500 C G 0.0 0.002 0.0794 +19 42912403 rs35938529 T A 0.0 0.0 0.0144 +19 44471209 rs365745 T A 0.8539 0.8452 0.4841 +19 44731222 rs10406980 T A 0.0288 0.1042 0.5227 +19 45818825 rs17875653 G C 0.007 0.0 0.0 +19 45882962 rs6966 T A 0.164 0.4425 0.6982 +19 47856140 rs1064202 G C 0.1213 0.4464 0.5522 +19 48374551 rs296365 C G 0.7376 0.7827 0.3805 +19 48519241 rs3745751 C G 0.0696 0.0764 0.2027 +19 48608598 rs2307279 C G 0.0497 0.2698 0.5779 +19 51743144 rs1803254 G C 0.0755 0.3373 0.295 +19 52003331 rs6509544 G C 0.8569 0.5149 0.9713 +19 52115645 rs3829655 G C 0.4225 0.5794 0.3275 +19 53577419 rs8105668 G C 0.8082 0.6032 0.9281 +19 54658001 rs1055234 C G 0.5149 0.3204 0.1634 +19 56390237 rs302453 A T 0.2187 0.1637 0.0189 +19 57985460 rs2074059 T A 0.6392 0.7014 0.6127 +19 59028162 rs35430780 G C 0.0567 0.0 0.003 +20 168728 rs4813043 T A 0.6093 0.4554 0.7867 +20 2077744 rs1418032 G C 0.2674 0.9157 0.9032 +20 8259959 rs2180532 T A 0.2684 0.4355 0.4062 +20 9496716 rs2232264 C G 0.1382 0.131 0.562 +20 15971797 rs11700097 G C 0.4314 0.25 0.0877 +20 23318014 rs1891687 T A 0.004 0.0873 0.407 +20 33764632 rs9574 C G 0.5169 0.372 0.8707 +20 44642406 rs2250889 G C 0.9543 0.7718 0.8283 +20 44671875 rs16985442 C G 0.0477 0.0 0.0303 +20 45186748 rs12617 T A 0.6859 0.9454 0.8502 +20 46264888 rs2230782 G C 0.1153 0.0218 0.003 +20 56534389 rs431750 T A 0.667 0.8879 0.9826 +21 32253513 rs9636845 A T 0.0885 0.4663 0.0045 +21 34729400 rs17875888 G C 0.0169 0.0 0.0 +21 37445526 rs998384 G C 0.3628 0.3264 0.2474 +21 37445739 rs998383 C G 0.3628 0.3264 0.2474 +21 37508878 rs879892 G C 0.4304 0.4335 0.0673 +21 38568009 rs1053966 G C 0.5129 0.8492 0.9024 +21 43523854 rs12482506 G C 0.0159 0.001 0.0008 +21 43620485 rs9975740 T A 0.1362 0.245 0.2625 +21 43628935 rs4148088 C G 0.0795 0.1954 0.0159 +21 43652782 rs915846 C G 0.3857 0.2917 0.27 +21 43673477 rs4148120 G C 0.1541 0.0744 0.0136 +21 43710909 rs914189 C G 0.1859 0.2163 0.385 +21 45564766 rs2838497 C G 0.0139 0.1081 0.2481 +21 46933164 rs17004786 G C 0.001 0.0 0.0832 +22 19948863 rs165656 G C 0.504 0.2688 0.4175 +22 19958710 rs7288060 T A 0.001 0.0 0.0469 +22 24479193 rs12166151 C G 0.0229 0.0 0.1036 +22 26231312 rs17704912 G C 0.0795 0.0 0.003 +22 26423124 rs6004901 G C 0.0348 0.004 0.2663 +22 29887186 rs710195 G C 0.6272 0.873 0.7564 +22 31060029 rs1005887 G C 0.2843 0.4385 0.7943 +22 39448725 rs35580576 T A 0.001 0.0 0.0 +22 41213267 rs138328 T A 0.4891 0.0754 0.3903 +22 45255637 rs6007344 G C 0.1899 0.4048 0.3207 +22 46608888 rs4253724 T A 0.2763 0.002 0.0651 +22 46608918 rs4253725 T A 0.2813 0.002 0.5643 +22 46613237 rs4253747 T A 0.2306 0.1865 0.5658 +22 50962782 rs140523 C G 0.6183 0.6677 0.6558 diff --git a/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/1000_Genomes_AF/InfiniumImmunoArray-24v2-0_A.1.3.1000_Genomes_AF.txt b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/1000_Genomes_AF/InfiniumImmunoArray-24v2-0_A.1.3.1000_Genomes_AF.txt new file mode 100644 index 0000000..4cc1b13 --- /dev/null +++ b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/1000_Genomes_AF/InfiniumImmunoArray-24v2-0_A.1.3.1000_Genomes_AF.txt @@ -0,0 +1,12487 @@ +chr position ID A1 A2 af_eur af_eas af_afr +1 1186502 rs6603785 A T 0.1143 0.2639 0.4637 +1 2413634 imm_1_2403494 G C 0.6133 0.7708 0.5045 +1 2420098 imm_1_2409958 A T 0.1163 0.1696 0.0817 +1 2426248 imm_1_2416108 G C 0.0209 0.003 0.0136 +1 2426598 imm_1_2416458 C G 0.0 0.0 0.0522 +1 2439685 imm_1_2429545 G C 0.5199 0.4881 0.1823 +1 2451984 imm_1_2441844 G C 0.002 0.0 0.0 +1 2454930 imm_1_2444790 G C 0.2127 0.5 0.7141 +1 2456417 imm_1_2446277 C G 0.0179 0.0 0.0 +1 2474313 imm_1_2464173 C G 0.0199 0.001 0.0008 +1 2477358 imm_1_2467218 T A 0.4761 0.5546 0.6407 +1 2487071 imm_1_2487347 G C 0.0 0.0 0.0688 +1 2491071 imm_1_2483347 C G 0.006 0.0 0.0 +1 2495495 rs11573997 G C 0.0169 0.005 0.0 +1 2498862 imm_1_2475556 G C 0.4901 0.5754 0.6286 +1 2510605 imm_1_2500465 C G 0.0507 0.0 0.0008 +1 2513678 imm_1_2503538 A T 0.4692 0.5675 0.8585 +1 2697542 imm_1_2687402 A T 0.0795 0.001 0.0287 +1 2707438 imm_1_2697298 A T 0.4414 0.3571 0.0885 +1 2723135 imm_1_2712995 C G 0.005 0.0 0.0008 +1 2726468 imm_1_2716328 T A 0.0219 0.0 0.0015 +1 2726864 imm_1_2716724 C G 0.0775 0.0 0.0015 +1 2735820 imm_1_2725680 C G 0.0179 0.1032 0.2746 +1 2756835 imm_1_2746695 G C 0.003 0.0 0.0008 +1 2763381 imm_1_2753241 G C 0.5825 0.5506 0.6732 +1 2768345 imm_1_2758205 T A 0.0089 0.0 0.0 +1 2770182 imm_1_2760042 A T 0.999 0.998 0.7549 +1 2775109 imm_1_2764969 C G 0.0109 0.0 0.0 +1 2778567 imm_1_2768427 C G 0.2555 0.3472 0.0575 +1 2779397 imm_1_2769257 C G 0.0994 0.002 0.0257 +1 2783815 imm_1_2773675 G C 0.5626 0.3919 0.0318 +1 2970930 rs12060482 T A 0.002 0.0 0.0847 +1 3225335 rs7526595 A T 0.004 0.0 0.3396 +1 3226616 rs10909927 G C 0.173 0.3036 0.3427 +1 4120556 rs4575054 T A 0.2783 0.4544 0.2057 +1 4490338 rs6676603 A T 0.4215 0.127 0.385 +1 4730283 rs4654582 T A 0.7783 0.6627 0.5514 +1 5373366 rs10915414 G C 0.0437 0.0685 0.2474 +1 5493392 rs12724170 G C 0.4364 0.249 0.5318 +1 6110789 rs2010057 A T 0.2167 0.0665 0.4168 +1 6279370 rs846111 G C 0.2604 0.1756 0.0227 +1 6568950 rs4908901 G C 0.5567 0.37 0.1997 +1 7567511 rs1725242 T A 0.8549 0.6438 0.789 +1 7739781 imm_1_7662368 G C 0.159 0.245 0.1029 +1 7741818 imm_1_7664405 C G 0.4513 0.6508 0.4501 +1 7762310 imm_1_7684897 C G 0.9384 0.999 0.8419 +1 7766701 imm_1_7689288 C G 0.0 0.0 0.0333 +1 7773380 imm_1_7695967 C G 0.4871 0.3651 0.2095 +1 7775272 imm_1_7697859 G C 0.007 0.001 0.0 +1 7775415 imm_1_7698002 G C 0.999 0.997 0.7716 +1 7780912 imm_1_7703499 G C 0.004 0.0 0.1233 +1 7788604 imm_1_7711191 C G 0.4622 0.4454 0.3177 +1 7837676 imm_1_7760263 G C 0.2197 0.4137 0.3033 +1 7837878 imm_1_7760465 C G 0.1561 0.0565 0.2398 +1 7853600 imm_1_7776187 C G 0.0 0.0 0.0144 +1 7857374 imm_1_7779961 G C 0.1551 0.0437 0.0098 +1 7858135 imm_1_7780722 G C 0.1551 0.0437 0.2095 +1 7859320 imm_1_7781907 C G 0.5795 0.1984 0.3336 +1 7863051 imm_1_7785638 A T 0.0915 0.0109 0.0204 +1 7880585 imm_1_7803172 A T 0.0 0.0 0.0477 +1 7897622 imm_1_7820209 A T 0.1551 0.0437 0.0098 +1 7913708 imm_1_7836295 A T 0.004 0.0 0.0 +1 7930554 imm_1_7853141 C G 0.6372 0.7431 0.8132 +1 7958247 rs11584201 C G 0.4433 0.0506 0.1021 +1 7960408 imm_1_7882995 T A 0.5905 0.7351 0.9546 +1 7974400 imm_1_7896987 C G 0.0278 0.5496 0.4818 +1 7979061 imm_1_7901648 A T 0.0 0.0 0.0386 +1 7982519 imm_1_7905106 A T 0.0239 0.5506 0.0053 +1 7999716 imm_1_7922303 C G 0.0 0.0 0.1838 +1 8011800 imm_1_7934387 G C 0.0149 0.5883 0.1082 +1 8028865 imm_1_7951452 G C 0.5934 0.6587 0.8805 +1 8065538 imm_1_7988125 G C 0.0 0.0 0.1974 +1 8070305 imm_1_7992892 G C 0.002 0.001 0.1029 +1 8078061 imm_1_8000648 A T 0.1352 0.0754 0.0961 +1 8079389 imm_1_8001976 C G 0.0 0.0 0.211 +1 8092275 imm_1_8014862 T A 0.0547 0.0595 0.0008 +1 8099171 imm_1_8021758 A T 0.0457 0.0 0.0008 +1 8111314 imm_1_8033901 G C 0.6054 0.6558 0.8805 +1 8121828 imm_1_8044415 G C 0.003 0.5952 0.0492 +1 8128093 imm_1_8050680 C G 0.001 0.0 0.2648 +1 8128653 imm_1_8051240 T A 0.0 0.0 0.202 +1 8134117 imm_1_8056704 G C 0.002 0.001 0.1929 +1 8148443 imm_1_8071030 G C 0.004 0.0 0.0015 +1 8164797 imm_1_8087384 G C 0.0457 0.0 0.0008 +1 8165667 imm_1_8088254 T A 0.83 0.2966 0.7738 +1 8168917 imm_1_8091504 T A 0.83 0.2937 0.8283 +1 8172492 imm_1_8095079 A T 0.831 0.2966 0.7723 +1 8173545 imm_1_8096132 C G 0.4682 0.004 0.1006 +1 8176250 imm_1_8098837 A T 0.002 0.0 0.438 +1 8181107 imm_1_8103694 A T 0.002 0.0 0.3964 +1 8182405 imm_1_8104992 C G 0.5288 0.996 0.503 +1 8184495 imm_1_8107082 G C 0.5358 0.997 0.9501 +1 8185678 imm_1_8108265 A T 0.001 0.0 0.0 +1 8187300 imm_1_8109887 T A 0.6879 0.997 0.9501 +1 8188997 imm_1_8111584 A T 0.661 0.9792 0.913 +1 8193584 imm_1_8116171 G C 0.6491 0.5228 0.2595 +1 9509821 rs10779726 G C 0.836 0.9464 0.7814 +1 10763246 rs651374 C G 0.6402 0.1002 0.2458 +1 11000721 rs6664866 T A 0.5567 0.7034 0.6452 +1 11848068 rs1537514 G C 0.1024 0.119 0.0885 +1 11851003 rs3818762 G C 0.2883 0.2232 0.1278 +1 11971256 1_11893843 C G 0.0 0.0 0.0098 +1 12104340 rs34286591 G C 0.0924 0.001 0.056 +1 12202095 rs755398 G C 0.5944 0.2748 0.5688 +1 12225351 rs652625 T A 0.0507 0.0099 0.3601 +1 12230631 rs559011 G C 0.003 0.0 0.1997 +1 12243377 rs542282 G C 0.2247 0.1548 0.1846 +1 12245732 rs4845897 T A 0.1481 0.1349 0.0159 +1 12248291 rs603151 G C 0.2306 0.1548 0.1846 +1 12249643 rs525891 A T 0.2137 0.1548 0.1967 +1 14048199 rs2495051 G C 0.7306 0.8909 0.9713 +1 15045765 rs6688730 C G 0.503 0.4871 0.1354 +1 15331603 rs7539545 A T 0.4175 0.4692 0.8495 +1 15333053 rs4633284 C G 0.2197 0.0149 0.4652 +1 17607501 imm_1_17480088 G C 0.173 0.001 0.0189 +1 17608545 imm_1_17481132 C G 0.0417 0.0744 0.1097 +1 17611548 imm_1_17484135 A T 0.828 0.999 0.7973 +1 17613838 imm_1_17486425 C G 0.171 0.001 0.0189 +1 17643572 imm_1_17516159 G C 0.9105 0.9464 0.8631 +1 17653954 imm_1_17526541 T A 0.661 0.6171 0.6074 +1 17659176 imm_1_17531763 A T 0.5537 0.5635 0.4796 +1 17660499 imm_1_17533086 G C 0.5537 0.5585 0.4607 +1 17662751 imm_1_17535338 C G 0.661 0.6141 0.5847 +1 17662907 imm_1_17535494 A T 0.661 0.6141 0.6014 +1 17665527 imm_1_17538114 C G 0.0129 0.0 0.0008 +1 17668976 imm_1_17541563 G C 0.1004 0.0526 0.1293 +1 17675713 imm_1_17548300 C G 0.0249 0.0 0.0204 +1 17916919 rs10788678 T A 0.5686 0.878 0.5545 +1 18176173 rs11203219 A T 0.0159 0.3938 0.0023 +1 18246140 rs12073092 T A 0.3439 0.1399 0.5371 +1 18257178 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0.6915 0.1899 +16 8392146 rs1868964 A T 0.0984 0.0327 0.0287 +16 9471268 rs8063998 G C 0.2157 0.5149 0.0567 +16 9755469 rs11646985 C G 0.508 0.4395 0.1664 +16 9755481 rs17568440 G C 0.337 0.1835 0.3646 +16 11004363 seq-rs6498126 G C 0.7793 0.6468 0.5514 +16 11006644 seq-rs11647308 G C 0.0447 0.0 0.003 +16 11013672 seq-rs12919139 C G 0.4135 0.3383 0.1672 +16 11017728 imm_16_10925229 G C 0.0497 0.1448 0.0507 +16 11037331 imm_16_10944832 C G 0.16 0.1181 0.2489 +16 11040492 seq-NOVEL-2553 C G 0.003 0.0 0.0121 +16 11041413 imm_16_10948914 C G 0.1372 0.2004 0.4402 +16 11042898 imm_16_10950399 G C 0.1292 0.13 0.1339 +16 11044933 imm_16_10952434 A T 0.1561 0.0724 0.2806 +16 11044953 imm_16_10952454 G C 0.001 0.0 0.0514 +16 11045278 imm_16_10952779 A T 0.162 0.13 0.4448 +16 11059363 imm_16_10966864 C G 0.1869 0.0744 0.3207 +16 11059776 imm_16_10967277 C G 0.0308 0.0 0.0424 +16 11076296 imm_16_10983797 T A 0.1322 0.125 0.0915 +16 11078558 imm_16_10986059 C G 0.0 0.001 0.059 +16 11081249 imm_16_10988750 C G 0.8201 0.8968 0.615 +16 11084244 imm_16_10991745 T A 0.006 0.0 0.3676 +16 11084511 imm_16_10992012 C G 0.001 0.0 0.0439 +16 11093321 imm_16_11000822 C G 0.4672 0.2996 0.8298 +16 11093476 imm_16_11000977 C G 0.0099 0.0 0.0 +16 11100333 imm_16_11007834 C G 0.1382 0.128 0.4032 +16 11118500 imm_16_11026001 G C 0.4125 0.3393 0.7269 +16 11120039 seq-NOVEL-3111 A T 0.003 0.0 0.031 +16 11125523 imm_16_11033024 G C 0.1292 0.1319 0.5098 +16 11135064 imm_16_11042565 C G 0.5616 0.4196 0.9728 +16 11135386 imm_16_11042887 G C 0.5616 0.4196 0.9743 +16 11140748 imm_16_11048249 G C 0.002 0.0 0.3971 +16 11141242 seq-rs28694699 T A 0.003 0.0 0.0772 +16 11143129 rs1985872 G C 0.4145 0.3442 0.7352 +16 11144209 imm_16_11051710 C G 0.1362 0.13 0.5234 +16 11145884 imm_16_11053385 C G 0.0706 0.0 0.003 +16 11153497 imm_16_11060998 G C 0.0974 0.1071 0.0439 +16 11153590 seq-NOVEL-3315 C G 0.0089 0.0 0.0015 +16 11156214 seq-NOVEL-3331 T A 0.003 0.0 0.0098 +16 11157220 imm_16_11064721 G C 1.0 1.0 1.0 +16 11161408 rs8061882 G C 0.1402 0.0754 0.0091 +16 11165542 rs7184615 G C 0.3658 0.2272 0.6422 +16 11167458 rs7198621 C G 0.334 0.2292 0.6399 +16 11172550 imm_16_11080051 G C 0.004 0.0 0.0 +16 11174823 imm_16_11082324 G C 0.001 0.0 0.1021 +16 11176668 imm_16_11084169 A T 0.1054 0.1319 0.0847 +16 11178070 imm_16_11085571 C G 0.1998 0.0625 0.0628 +16 11185799 imm_16_11093300 G C 0.0606 0.1121 0.0719 +16 11189148 imm_16_11096649 G C 0.4245 0.4335 0.7027 +16 11192379 imm_16_11099880 G C 0.4225 0.3373 0.5461 +16 11197637 imm_16_11105138 C G 0.001 0.0 0.1165 +16 11199984 imm_16_11107485 A T 0.006 0.0 0.0 +16 11203565 imm_16_11111066 G C 0.4205 0.3542 0.5371 +16 11208658 imm_16_11116159 C G 0.0 0.0 0.146 +16 11217107 imm_16_11124608 G C 0.6252 0.4702 0.9766 +16 11217107 rs8060411 G C 0.6252 0.4702 0.9766 +16 11223454 imm_16_11130955 C G 0.5219 0.2917 0.3858 +16 11224937 imm_16_11132438 C G 0.001 0.0 0.0469 +16 11225064 imm_16_11132565 C G 0.2515 0.0635 0.1914 +16 11238202 seq-NOVEL-3892 C G 0.002 0.0 0.0091 +16 11238991 rs4322688 C G 0.3579 0.2242 0.3132 +16 11239689 imm_16_11147190 C G 0.1103 0.1558 0.3003 +16 11239978 imm_16_11147479 A T 0.3579 0.2242 0.3154 +16 11240854 rs35294447 A T 0.3539 0.2361 0.292 +16 11254478 imm_16_11161979 G C 0.1551 0.0952 0.3555 +16 11254495 imm_16_11161996 C G 0.0 0.0 0.0651 +16 11255254 imm_16_11162755 A T 0.1551 0.0942 0.3404 +16 11261183 imm_16_11168684 G C 0.0775 0.0 0.003 +16 11265201 imm_16_11172702 C G 0.1083 0.002 0.0061 +16 11268900 imm_16_11176401 C G 0.001 0.0 0.0 +16 11277130 seq-NOVEL-4110 A T 0.001 0.0 0.0938 +16 11278073 seq-NOVEL-4121 C G 0.001 0.0 0.0938 +16 11279248 seq-NOVEL-4138 C G 0.001 0.0 0.0991 +16 11279977 imm_16_11187478 G C 0.9414 1.0 0.997 +16 11280544 seq-rs11641320 C G 0.0835 0.121 0.0802 +16 11282712 imm_16_11190213 A T 0.0189 0.0 0.056 +16 11286797 imm_16_11194298 G C 0.1322 0.2202 0.4138 +16 11288195 imm_16_11195696 C G 0.0 0.0 0.0401 +16 11288570 seq-NOVEL-4264 G C 0.002 0.0 0.056 +16 11288824 imm_16_11196325 G C 0.5129 0.5377 0.5817 +16 11288971 imm_16_11196472 C G 0.661 0.622 0.6293 +16 11290407 imm_16_11197908 C G 0.66 0.621 0.587 +16 11292746 imm_16_11200247 A T 0.0 0.0 0.0393 +16 11302123 seq-NOVEL-4379 C G 0.0 0.0 0.0333 +16 11312399 rs2113261 C G 0.325 0.624 0.3457 +16 11315639 rs4781046 T A 0.1312 0.4028 0.0121 +16 11318816 imm_16_11226317 G C 0.7078 0.7798 0.5166 +16 11318816 rs1690492 G C 0.7078 0.7798 0.5166 +16 11321723 imm_16_11229224 G C 0.6034 0.6448 0.4554 +16 11321723 rs1646071 G C 0.6034 0.6448 0.4554 +16 11332149 imm_16_11239650 C G 0.0318 0.4474 0.1989 +16 11340670 rs396753 G C 0.5765 0.6845 0.6384 +16 11343942 imm_16_11251443 C G 0.5189 0.2718 0.2587 +16 11343942 rs149597 C G 0.5189 0.2718 0.2587 +16 11348211 imm_16_11255712 C G 0.2694 0.2659 0.0446 +16 11355104 imm_16_11262605 A T 0.2664 0.003 0.2277 +16 11355104 rs56350515 A T 0.2664 0.003 0.2277 +16 11355798 imm_16_11263299 G C 0.0209 0.5913 0.0318 +16 11363389 rs7191538 C G 0.5328 0.2748 0.2655 +16 11366003 imm_16_11273504 G C 0.7018 0.8889 0.475 +16 11368616 imm_16_11276117 T A 0.2575 0.002 0.1936 +16 11369263 imm_16_11276764 T A 0.4503 0.0446 0.3699 +16 11369696 imm_16_11277197 C G 0.0099 0.0 0.0008 +16 11377006 imm_16_11284507 T A 0.002 0.0 0.0 +16 11394402 imm_16_11301903 T A 0.5736 0.6806 0.6528 +16 11394402 rs4238603 T A 0.5736 0.6806 0.6528 +16 11396143 imm_16_11303644 C G 0.1451 0.6776 0.1725 +16 11396143 rs880341 C G 0.1451 0.6776 0.1725 +16 11397107 imm_16_11304608 G C 0.5746 0.6806 0.7224 +16 11397107 rs1019551 G C 0.5746 0.6806 0.7224 +16 11406544 imm_16_11314045 G C 0.16 0.0417 0.0741 +16 11414196 imm_16_11321697 C G 0.7445 0.998 0.4523 +16 11417119 imm_16_11324620 T A 0.173 0.6577 0.1672 +16 11417802 imm_16_11325303 G C 0.0179 0.0 0.0 +16 11422899 imm_16_11330400 C G 0.0199 0.0 0.0008 +16 11426972 imm_16_11334473 G C 0.7356 0.7163 0.6785 +16 11427123 imm_16_11334624 C G 0.7356 0.7163 0.677 +16 11428643 imm_16_11336144 C G 0.1581 0.0427 0.0083 +16 11434842 imm_16_11342343 C G 0.5964 0.4534 0.4191 +16 11437316 imm_16_11344817 C G 0.2545 0.001 0.2156 +16 11438221 imm_16_11345722 T A 0.2555 0.001 0.298 +16 11439679 imm_16_11347180 C G 0.497 0.2837 0.4009 +16 11439803 imm_16_11347304 G C 0.3926 0.2847 0.3601 +16 11455181 imm_16_11362682 G C 0.6243 0.8194 0.3707 +16 11457148 imm_16_11364649 T A 1.0 1.0 0.8601 +16 11461781 imm_16_11369282 G C 0.1431 0.001 0.0045 +16 11464332 imm_16_11371833 G C 0.7416 0.6349 0.854 +16 11465644 imm_16_11373145 G C 0.1034 0.002 0.0098 +16 11468274 imm_16_11375775 G C 0.1252 0.0 0.003 +16 11471414 imm_16_11378915 C G 0.4245 0.2569 0.2685 +16 11472642 imm_16_11380143 T A 0.5507 0.256 0.2776 +16 11474049 imm_16_11381550 G C 0.6272 0.2649 0.7806 +16 11475039 imm_16_11382540 C G 0.1103 0.001 0.2284 +16 11475673 rs11860060 C G 0.667 0.2649 0.7337 +16 12003948 rs7204312 C G 0.0308 0.1657 0.2126 +16 12058832 rs11570136 T A 0.3439 0.5536 0.0711 +16 12060784 rs11570153 C G 0.0 0.0 0.0628 +16 12323309 rs830717 C G 0.5169 0.2758 0.1203 +16 13032136 rs7499101 G C 0.2783 0.3502 0.1354 +16 13033361 rs961946 T A 0.1889 0.1607 0.0189 +16 13245367 rs150070 G C 0.6819 0.7411 0.3797 +16 13334465 rs9928389 G C 0.162 0.2034 0.0953 +16 13613166 rs7194750 A T 0.7177 0.9613 0.7716 +16 13839866 rs2187680 T A 0.7535 0.8681 0.5098 +16 13843843 rs2187682 T A 0.171 0.125 0.118 +16 13863492 rs2213302 C G 0.7515 0.877 0.5053 +16 13937872 rs7197456 G C 0.0089 0.0 0.3858 +16 14302008 rs226781 C G 0.0586 0.2857 0.0628 +16 16140041 rs17205838 G C 0.172 0.0863 0.0416 +16 17253548 rs9934960 C G 0.6909 0.3056 0.3404 +16 19375914 rs8050983 A T 0.0477 0.0278 0.3313 +16 20059843 rs1925501 T A 0.2366 0.3254 0.2095 +16 20674492 rs151222 G C 0.0726 0.2133 0.0257 +16 23390201 rs2303153 G C 0.4831 0.8562 0.8147 +16 23682271 rs12447304 C G 0.0636 0.0 0.0038 +16 23925153 rs8051946 T A 0.9414 1.0 0.8351 +16 24198850 rs198142 T A 0.0547 0.0347 0.0582 +16 26214282 rs6497934 C G 0.3807 0.4653 0.323 +16 26532224 rs4581702 A T 0.331 0.1617 0.267 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imm_16_28508687 G C 0.1233 0.004 0.0794 +16 28631383 16_28538884 C G 0.0 0.0972 0.0 +16 28843327 imm_16_28750828 C G 0.0139 0.0 0.0 +16 28844068 imm_16_28751569 T A 0.6093 0.7778 0.9319 +16 28847149 imm_16_28754650 G C 0.329 0.126 0.2277 +16 28855522 imm_16_28763023 G C 0.329 0.126 0.2277 +16 28985731 imm_16_28893232 T A 0.0119 0.2361 0.2269 +16 28998111 imm_16_28905612 T A 0.1938 0.1359 0.0061 +16 29023105 imm_16_28930606 G C 0.6521 0.3988 0.2557 +16 30078492 rs9783783 G C 0.499 0.3661 0.618 +16 30169393 rs12927190 C G 0.5616 0.8998 0.9501 +16 30169761 rs7195182 G C 0.5616 0.8998 0.8306 +16 30529315 imm_16_30436816 G C 0.0 0.0 0.1339 +16 30589667 imm_16_30497168 A T 0.0169 0.0 0.0008 +16 30631105 imm_16_30538606 A T 0.0129 0.0 0.0008 +16 30656594 imm_16_30564095 T A 0.3708 0.1141 0.9387 +16 30714828 imm_16_30622329 A T 0.2823 0.1111 0.9455 +16 30727853 imm_16_30635354 C G 0.0129 0.0 0.0 +16 30737541 imm_16_30645042 T A 0.002 0.0 0.0008 +16 30770267 imm_16_30677768 C G 1.0 1.0 0.8805 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C G 0.0129 0.0 0.0 +16 31182455 imm_16_31089956 G C 0.3111 0.255 0.0363 +16 31203529 imm_16_31111030 G C 0.3072 0.254 0.0363 +16 31209224 imm_16_31116725 C G 0.0 0.0 0.0552 +16 31229460 imm_16_31136961 G C 0.0 0.0 0.0431 +16 31283323 imm_16_31190824 C G 0.1392 0.0149 0.1165 +16 31287148 imm_16_31194649 A T 0.1402 0.0149 0.3533 +16 31287427 imm_16_31194928 A T 0.2684 0.0179 0.8374 +16 31301910 imm_16_31209411 G C 0.1421 0.0278 0.5976 +16 31343670 imm_16_31251171 G C 0.0219 0.001 0.0 +16 31355360 imm_16_31262861 T A 0.675 0.6835 0.9501 +16 31371193 imm_16_31278694 C G 0.9036 0.9871 0.9312 +16 49771744 rs8048073 C G 0.3459 0.2609 0.5446 +16 50702042 imm_16_49259543 G C 0.001 0.0 0.4773 +16 50718403 imm_16_49275904 C G 0.7416 0.1022 0.4879 +16 50723371 imm_16_49280872 A T 0.7396 0.2212 0.6475 +16 50724087 imm_16_49281588 G C 0.7386 0.2222 0.6551 +16 50726236 imm_16_49283737 G C 0.0109 0.0 0.0008 +16 50728498 imm_16_49285999 G C 0.0408 0.0 0.0008 +16 50731895 imm_16_49289396 G C 0.0 0.0 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rs4253724 T A 0.2763 0.002 0.0651 +22 46608918 rs4253725 T A 0.2813 0.002 0.5643 +22 46613237 rs4253747 T A 0.2306 0.1865 0.5658 +22 46652516 exm1617823 T A 0.002 0.001 0.0 +22 46655779 exm1617965 G C 0.1233 0.001 0.0802 +22 46655919 exm1617966 T A 0.001 0.0 0.0 +22 46658471 exm1618077 G C 0.0 0.0 0.0 +22 46724650 exm2015831 G C 0.0 0.003 0.0 +22 46725974 exm1618350 C G 0.0 0.0099 0.0 +22 46746276 exm2015856 C G 0.0 0.0 0.0 +22 46760481 exm1618494 C G 0.2455 0.005 0.5492 +22 46762970 exm1618550 G C 0.001 0.0 0.0 +22 46932032 exm1619080 T A 0.002 0.0 0.0 +22 47106996 exm1619303 C G 0.002 0.0 0.0008 +22 47189678 exm1619369 C G 0.0199 0.0 0.0008 +22 50169346 exm2255261 G C 0.0 0.0 0.0076 +22 50217649 exm1619708 C G 0.0 0.0 0.0151 +22 50278356 exm1619786 C G 0.0 0.0 0.0015 +22 50313441 exm1620056 G C 0.001 0.0 0.0 +22 50354783 exm1620160 C G 0.0 0.0 0.0083 +22 50356432 exm1620180 A T 0.0 0.0 0.0076 +22 50530501 exm1620547 A T 0.2356 0.255 0.1301 +22 50632055 exm1620861 G C 0.0 0.0 0.0015 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b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/1000_Genomes_AF/InfiniumOmniExpressExome-8v1-6_A1.1.3.1000_Genomes_AF.txt @@ -0,0 +1,11315 @@ +chr position ID A1 A2 af_eur af_eas af_afr +1 889403 exm355 T A 0.0 0.0 0.0219 +1 892388 exm396 C G 0.0 0.0 0.0008 +1 905669 exm636 C G 0.0 0.0 0.003 +1 907676 exm714 A T 0.0 0.0 0.0038 +1 909015 exm767 G C 0.0 0.0 0.0008 +1 979748 exm1081 A T 0.0467 0.0079 0.0008 +1 980863 exm1101 C G 0.0 0.0 0.0015 +1 1120370 exm1640 C G 0.0 0.0 0.1006 +1 1120377 exm1641 T A 0.0179 0.0 0.003 +1 1139251 exm1687 C G 0.0 0.0 0.0053 +1 1219382 exm2062 C G 0.0 0.0 0.0522 +1 1222279 exm2113 C G 0.0 0.0 0.0015 +1 1222528 exm2130 A T 0.002 0.0 0.0 +1 1223385 exm2183 G C 0.0229 0.6111 0.354 +1 1226797 exm2259 C G 0.002 0.0 0.0 +1 1231245 exm2330 C G 0.0 0.0 0.0076 +1 1246018 exm1706581 C G 0.0 0.0069 0.0 +1 1262635 exm2695 T A 0.001 0.0 0.0 +1 1268701 exm2883 C G 0.0 0.001 0.0 +1 1334475 exm3317 G C 0.0308 0.0 0.0 +1 1334519 exm3320 G C 0.0179 0.001 0.003 +1 1337539 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exm1607941 G C 0.002 0.0 0.0 +22 38508172 exm2010232 G C 0.0 0.0149 0.0 +22 38882187 exm1608501 C G 0.001 0.0 0.0 +22 39263050 exm1609063 G C 0.0 0.0 0.0091 +22 39421122 exm1609288 G C 0.002 0.0 0.0015 +22 39448725 rs35580576 T A 0.001 0.0 0.0 +22 39497454 exm1609542 G C 0.4771 0.3155 0.8752 +22 40161282 exm1610476 G C 0.0 0.0 0.0 +22 40661729 exm1610750 G C 0.005 0.0 0.0 +22 40750289 exm1610898 A T 0.0 0.0 0.0582 +22 40755034 exm2011784 C G 0.0 0.0 0.0 +22 40801688 exm2011823 G C 0.0 0.001 0.0008 +22 40816889 exm1611282 C G 0.004 0.0 0.0008 +22 40819629 exm1611290 G C 0.0 0.0 0.0083 +22 41213267 rs138328 T A 0.4891 0.0754 0.3903 +22 41322392 exm1611620 C G 0.003 0.0 0.0 +22 41513774 exm1611673 C G 0.001 0.0159 0.0008 +22 41546131 exm2012425 T A 0.0 0.0 0.003 +22 41568649 exm2255205 C G 0.0 0.0 0.0023 +22 41572269 exm1611836 C G 0.003 0.0 0.0 +22 41605809 exm1611984 G C 0.0 0.0129 0.0 +22 41652257 exm1612202 G C 0.0 0.0 0.0197 +22 41660751 exm2012652 C G 0.0 0.0 0.0106 +22 41911805 exm1612570 G C 0.001 0.0 0.0 +22 42095711 exm1612933 G C 0.0109 0.0278 0.0061 +22 42172118 exm1613024 T A 0.001 0.0 0.0507 +22 42423110 exm1613457 G C 0.671 0.8542 0.9455 +22 42459001 exm1613489 A T 0.0 0.0 0.0015 +22 42463140 exm1613505 G C 0.002 0.0 0.0 +22 42611265 exm1614112 C G 0.0129 0.0159 0.003 +22 42805444 exm1614146 G C 0.001 0.0 0.1157 +22 42956273 exm1614300 T A 0.001 0.0 0.0234 +22 42981961 exm1614375 T A 0.0 0.0 0.0008 +22 43195045 exm1614574 C G 0.0 0.0 0.0015 +22 43195114 exm1614581 G C 0.006 0.0 0.003 +22 43529094 exm1614910 C G 0.0 0.0 0.0227 +22 43529314 exm1614928 G C 0.663 0.6369 0.2216 +22 43564050 exm1615025 G C 0.005 0.0 0.0008 +22 43623418 exm2014748 G C 0.0 0.0099 0.0 +22 43831058 exm1615423 G C 0.0 0.0 0.003 +22 45243896 exm1616577 G C 0.0 0.0 0.0038 +22 45255637 exm1616610 G C 0.1899 0.4048 0.3207 +22 45255637 rs6007344 G C 0.1899 0.4048 0.3207 +22 45258242 exm1616648 G C 0.0 0.0 0.0015 +22 45258373 exm1616670 G C 0.0348 0.0 0.0015 +22 45683116 exm1616988 A T 0.0 0.0 0.0522 +22 45691446 exm1617030 T A 0.0 0.0 0.0015 +22 45740462 exm1617131 C G 0.0 0.0288 0.0 +22 45795041 exm1617218 A T 0.001 0.0 0.0 +22 46327122 exm1617624 G C 0.0 0.0 0.0015 +22 46608888 rs4253724 T A 0.2763 0.002 0.0651 +22 46608918 rs4253725 T A 0.2813 0.002 0.5643 +22 46613237 rs4253747 T A 0.2306 0.1865 0.5658 +22 46652516 exm1617823 T A 0.002 0.001 0.0 +22 46655779 exm1617965 G C 0.1233 0.001 0.0802 +22 46655919 exm1617966 T A 0.001 0.0 0.0 +22 46658471 exm1618077 G C 0.0 0.0 0.0 +22 46724650 exm2015831 G C 0.0 0.003 0.0 +22 46725974 exm1618350 C G 0.0 0.0099 0.0 +22 46746276 exm2015856 C G 0.0 0.0 0.0 +22 46760481 exm1618494 C G 0.2455 0.005 0.5492 +22 46762970 exm1618550 G C 0.001 0.0 0.0 +22 46932032 exm1619080 T A 0.002 0.0 0.0 +22 47106996 exm1619303 C G 0.002 0.0 0.0008 +22 47189678 exm1619369 C G 0.0199 0.0 0.0008 +22 50169346 exm2255261 G C 0.0 0.0 0.0076 +22 50217649 exm1619708 C G 0.0 0.0 0.0151 +22 50313441 exm1620056 G C 0.001 0.0 0.0 +22 50354783 exm1620160 C G 0.0 0.0 0.0083 +22 50356432 exm1620180 A T 0.0 0.0 0.0076 +22 50530501 exm1620547 A T 0.2356 0.255 0.1301 +22 50632055 exm1620861 G C 0.0 0.0 0.0015 +22 50649223 exm1621006 G C 0.001 0.0 0.0 +22 50660214 exm2017001 C G 0.0 0.0 0.0 +22 50678739 exm2017060 T A 0.0 0.004 0.0 +22 50682361 exm2017067 C G 0.001 0.0 0.0 +22 50900141 exm1622741 G C 0.0 0.0 0.003 +22 50901349 exm1622791 C G 0.001 0.0 0.0008 +22 50903029 exm1622815 T A 0.0 0.0 0.0265 +22 50959456 exm2255274 C G 0.0 0.0 0.0113 +22 50962782 exm1623457 C G 0.6183 0.6677 0.6558 +22 50962782 rs140523 C G 0.6183 0.6677 0.6558 +22 51011376 exm1623703 G C 0.1143 0.501 0.6679 +22 51064039 exm1623987 G C 0.5288 0.3214 0.3578 +22 51065266 exm1624014 G C 0.0 0.0 0.0008 diff --git a/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/1000_Genomes_AF/MEG_AllofUs_20002558X351448_A2.1.3.1000_Genomes_AF.txt b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/1000_Genomes_AF/MEG_AllofUs_20002558X351448_A2.1.3.1000_Genomes_AF.txt new file mode 100644 index 0000000..c77970e --- /dev/null +++ b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/1000_Genomes_AF/MEG_AllofUs_20002558X351448_A2.1.3.1000_Genomes_AF.txt @@ -0,0 +1,85683 @@ +chr position ID A1 A2 af_eur af_eas af_afr +1 770377 rs112563271 A T 0.0089 0.2431 0.0008 +1 805556 JHU_1.805555 T A 0.0924 0.3175 0.0855 +1 885155 rs78729032 C G 0.0 0.0169 0.0 +1 889403 exm355 T A 0.0 0.0 0.0219 +1 892388 exm396 C G 0.0 0.0 0.0008 +1 905669 exm636 C G 0.0 0.0 0.003 +1 907676 exm714 A T 0.0 0.0 0.0038 +1 909015 exm767 G C 0.0 0.0 0.0008 +1 979748 exm1081 A T 0.0467 0.0079 0.0008 +1 979748 rs113288277 A T 0.0467 0.0079 0.0008 +1 980863 exm1101 C G 0.0 0.0 0.0015 +1 1107842 rs11260535 G C 0.0646 0.6974 0.149 +1 1120370 exm1640 C G 0.0 0.0 0.1006 +1 1120370 JHU_1.1120369 C G 0.0 0.0 0.1006 +1 1120377 exm1641 T A 0.0179 0.0 0.003 +1 1139251 exm1687 C G 0.0 0.0 0.0053 +1 1142254 JHU_1.1142253 C G 0.0 0.0 0.0431 +1 1222279 exm2113 C G 0.0 0.0 0.0015 +1 1222528 exm2130 A T 0.002 0.0 0.0 +1 1225959 JHU_1.1225958 C G 0.1243 0.877 0.7148 +1 1226797 exm2259 C G 0.002 0.0 0.0 +1 1231245 exm2330 C G 0.0 0.0 0.0076 +1 1241913 rs139103600 C G 0.0 0.0099 0.0 +1 1246018 exm1706581 C G 0.0 0.0069 0.0 +1 1262635 exm2695 T A 0.001 0.0 0.0 +1 1308871 JHU_1.1308870 A T 0.9602 0.9147 0.9781 +1 1311542 JHU_1.1311541 G C 0.8111 0.0208 0.1823 +1 1334519 exm3320 G C 0.0179 0.001 0.003 +1 1337539 exm3332 T A 0.0 0.0 0.0068 +1 1363807 JHU_1.1363806 G C 0.0 0.0 0.0461 +1 1373482 JHU_1.1373481 G C 0.1521 0.9623 0.2005 +1 1395229 JHU_1.1395228 G C 0.0 0.0 0.0424 +1 1420077 JHU_1.1420076 A T 0.0159 0.0099 0.0174 +1 1447123 JHU_1.1447122 G C 0.0 0.0 0.0514 +1 1506118 rs118064867 C G 0.0 0.0496 0.0 +1 1650885 rs201091435 T A 0.0 0.0 0.0015 +1 1669511 JHU_1.1669510 C G 0.001 0.0 0.0303 +1 1698876 rs79955828 A T 0.002 0.1121 0.0 +1 1713956 JHU_1.1713955 G C 0.0 0.0 0.028 +1 1847994 exm4647 C G 0.0 0.0 0.0008 +1 1848197 exm4656 G C 0.0 0.0 0.0333 +1 1848197 rs74773083 G C 0.0 0.0 0.0333 +1 1891263 JHU_1.1891262 A T 0.0954 0.3313 0.0091 +1 1897889 exm4936 G C 0.001 0.0 0.1195 +1 1902133 exm4966 G C 0.0 0.0 0.003 +1 1905557 exm5009 G C 0.0 0.0 0.0144 +1 1971389 JHU_1.1971388 G C 0.663 0.2877 0.382 +1 1985513 rs13303289 C G 0.1382 0.3214 0.6838 +1 2063552 rs141109084 G C 0.0 0.0327 0.0 +1 2063841 JHU_1.2063840 C G 0.004 0.0 0.0862 +1 2063841 rs72925854 C G 0.004 0.0 0.0862 +1 2075672 exm5180 C G 0.002 0.0 0.0 +1 2125086 exm5277 G C 0.0 0.0 0.0023 +1 2156715 JHU_1.2156714 C G 0.0 0.0 0.0144 +1 2170517 1:2170517-G-C C G 0.0 0.0 0.0 +1 2220070 JHU_1.2220069 T A 0.2773 0.127 0.059 +1 2231966 rs55710545 G C 0.1909 0.1062 0.1067 +1 2266714 rs2643900 G C 0.2137 0.0972 0.3033 +1 2283313 rs2843130 C G 0.165 0.2312 0.025 +1 2308517 rs2843162 C G 0.8907 0.8661 0.9592 +1 2324881 JHU_1.2324880 G C 0.1491 0.2679 0.4213 +1 2338223 exm5606 C G 0.005 0.0 0.0 +1 2417930 rs114871065 G C 0.0169 0.004 0.0431 +1 2419415 rs78283022 C G 0.0159 0.006 0.0287 +1 2452979 rs12073504 C G 0.006 0.0288 0.0272 +1 2453758 JHU_1.2453757 C G 0.002 0.0 0.0514 +1 2469836 JHU_1.2469835 C G 0.0 0.0 0.0764 +1 2535648 exm6307 C G 0.002 0.0 0.0 +1 2561955 1:2561955-C-G G C 0.0 0.0149 0.0 +1 2632200 JHU_1.2632199 C G 0.0 0.0 0.0272 +1 2684840 1:2684840-A-T T A 0.0229 0.0 0.0008 +1 2697542 rs11590361 A T 0.0795 0.001 0.0287 +1 2812244 rs10909834 G C 0.2147 0.3581 0.2451 +1 2821050 rs114116939 G C 0.0 0.0 0.056 +1 2879460 JHU_1.2879459 G C 0.2525 0.1538 0.0204 +1 2887855 rs60542493 G C 0.005 0.0 0.1195 +1 2993807 rs2981888 C G 0.7048 0.9573 0.6747 +1 2994336 rs4648359 G C 0.5139 0.879 0.3759 +1 3015358 JHU_1.3015357 G C 0.2843 0.2718 0.3313 +1 3018995 rs74633240 G C 0.0089 0.2202 0.0136 +1 3043044 JHU_1.3043043 C G 0.0109 0.2183 0.264 +1 3053030 rs4648364 C G 0.1958 0.4504 0.1082 +1 3062333 JHU_1.3062332 C G 0.001 0.0 0.0651 +1 3110417 JHU_1.3110416 C G 0.9692 1.0 0.9675 +1 3115721 JHU_1.3115720 C G 0.7913 0.5575 0.7844 +1 3115853 JHU_1.3115852 T A 0.0 0.0 0.1589 +1 3192066 JHU_1.3192065 A T 0.0 0.0 0.0219 +1 3226027 rs140812042 G C 0.0 0.0258 0.0 +1 3226539 rs59127130 T A 0.0457 0.001 0.1921 +1 3227175 rs2483259 C G 0.2386 0.0119 0.0522 +1 3274986 rs78844001 A T 0.0 0.0317 0.0 +1 3345145 rs2483242 A T 0.4046 0.2093 0.7708 +1 3363963 JHU_1.3363962 A T 0.0388 0.1329 0.1611 +1 3421658 rs2821009 A T 0.3201 0.6627 0.6891 +1 3432278 rs12045137 C G 0.1899 0.4206 0.3873 +1 3434984 rs2794362 G C 0.6849 0.7629 0.7617 +1 3499296 rs75898828 C G 0.0169 0.0863 0.0227 +1 3506326 JHU_1.3506325 T A 0.0139 0.2163 0.0159 +1 3506326 rs57453372 T A 0.0139 0.2163 0.0159 +1 3522140 JHU_1.3522139 A T 0.3509 0.4246 0.4274 +1 3532299 JHU_1.3532298 G C 0.3022 0.3333 0.0514 +1 3546429 JHU_1.3546428 C G 0.0 0.0 0.0061 +1 3548832 exm7253 G C 0.0547 0.002 0.0348 +1 3551592 exm7274 C G 0.001 0.0 0.0 +1 3579466 rs12118148 C G 0.2406 0.3462 0.3207 +1 3589880 JHU_1.3589879 G C 0.3926 0.5476 0.6036 +1 3603695 JHU_1.3603694 A T 0.0298 0.2113 0.3684 +1 3603926 JHU_1.3603925 C G 0.2425 0.5069 0.3442 +1 3622636 rs12086279 A T 0.2763 0.0565 0.0847 +1 3635465 rs3765767 G C 0.5318 0.3284 0.1256 +1 3671607 rs72846550 C G 0.004 0.001 0.4599 +1 3680656 JHU_1.3680655 G C 0.0 0.0 0.152 +1 3683914 exm7617 T A 0.003 0.0883 0.003 +1 3697675 exm7647 G C 0.002 0.0 0.0 +1 3700579 exm7668 T A 0.0 0.0 0.003 +1 3703337 JHU_1.3703336 G C 0.6481 0.3998 0.3457 +1 3706559 rs72846586 G C 0.001 0.0 0.2474 +1 3721859 rs6691991 G C 0.2555 0.0496 0.4508 +1 3727517 rs67003509 A T 0.1173 0.001 0.2587 +1 3743350 rs58111155 G C 0.0179 0.0883 0.0151 +1 3753136 exm7844 A T 0.4284 0.3383 0.0605 +1 3761485 exm7891 T A 0.0 0.0 0.0159 +1 3761487 exm7892 C G 0.001 0.0 0.0 +1 3785423 rs34874218 C G 0.1461 0.006 0.0038 +1 3796152 rs56070860 C G 0.33 0.119 0.1982 +1 3802771 rs11584721 G C 0.1392 0.2331 0.0991 +1 3809299 rs79308453 T A 0.0388 0.0 0.0159 +1 4000041 rs12405341 G C 0.1113 0.0198 0.1732 +1 4001464 rs35304605 G C 0.003 0.244 0.1967 +1 4078945 rs7548273 G C 0.167 0.0486 0.3903 +1 4088407 JHU_1.4088406 C G 0.2147 0.1389 0.3631 +1 4088480 JHU_1.4088479 G C 0.0338 0.1438 0.2247 +1 4106651 rs10753347 G C 0.2157 0.1984 0.6256 +1 4108150 rs77495118 T A 0.001 0.0863 0.0113 +1 4118862 JHU_1.4118861 G C 0.0 0.0 0.0628 +1 4134715 rs6426384 T A 0.2455 0.4077 0.2231 +1 4142285 JHU_1.4142284 C G 0.0 0.0 0.0416 +1 4159681 JHU_1.4159680 T A 0.1421 0.003 0.1346 +1 4159681 rs77384844 T A 0.1421 0.003 0.1346 +1 4217760 rs191027691 T A 0.0 0.0228 0.0 +1 4220472 JHU_1.4220471 G C 0.0 0.0 0.0219 +1 4275876 rs4615813 G C 0.9692 0.9871 0.7595 +1 4368441 JHU_1.4368440 A T 0.8131 0.8006 0.8026 +1 4391871 JHU_1.4391870 C G 0.0 0.0 0.0318 +1 4398059 JHU_1.4398058 G C 0.2296 0.4087 0.3979 +1 4401510 JHU_1.4401509 G C 0.0 0.0 0.0408 +1 4452404 JHU_1.4452403 T A 0.007 0.4177 0.2587 +1 4468118 rs17451926 T A 0.0835 0.1002 0.0061 +1 4472376 rs114060995 T A 0.0199 0.0 0.0 +1 4528773 rs1878054 T A 0.2575 0.1815 0.3041 +1 4530402 JHU_1.4530401 A T 0.0 0.0 0.0242 +1 4569436 rs780569 T A 0.7326 0.8442 0.5446 +1 4588789 rs116105448 A T 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5688024 rs11820502 G C 0.3181 0.6171 0.8487 +11 5692032 JHU_11.5692031 C G 0.2008 0.4296 0.6324 +11 5696672 rs190736090 G C 0.0 0.0 0.0144 +11 5700399 exm883577 C G 0.004 0.0 0.0 +11 5757930 exm883711 C G 0.0 0.0 0.0038 +11 5760006 JHU_11.5760005 T A 0.502 0.2431 0.3434 +11 5772331 JHU_11.5772330 C G 0.1123 0.0 0.0303 +11 5776484 exm883786 A T 0.2783 0.1974 0.1498 +11 5778636 JHU_11.5778635 A T 0.0477 0.0 0.0265 +11 5781188 JHU_11.5781187 C G 0.0378 0.0089 0.0166 +11 5817632 JHU_11.5817631 A T 0.0089 0.0 0.062 +11 5824435 11:5824435-T-A A T 0.001 0.0109 0.0 +11 5842283 exm883965 T A 0.002 0.0 0.0008 +11 5862619 exm884017 A T 0.0 0.0 0.0318 +11 5862984 exm884047 G C 0.3728 0.4593 0.379 +11 5907873 JHU_11.5907872 G C 0.001 0.0 0.1831 +11 5910347 rs11039472 G C 0.1262 0.0 0.0681 +11 5989191 exm884221 C G 0.001 0.0 0.0371 +11 6015011 rs73404126 T A 0.0258 0.004 0.0688 +11 6073685 rs113375247 T A 0.0288 0.0 0.0 +11 6133714 rs11040752 G C 0.001 0.0 0.0514 +11 6156162 JHU_11.6156161 A T 0.0 0.0 0.0295 +11 6188361 rs72900479 T A 0.1054 0.0119 0.0113 +11 6191243 exm884504 A T 0.0 0.0 0.1619 +11 6192589 JHU_11.6192588 G C 0.0 0.0 0.0227 +11 6197225 JHU_11.6197224 C G 0.0149 0.0 0.0356 +11 6261544 exm2219034 C G 0.0 0.005 0.0 +11 6263057 rs137959615 G C 0.0 0.0109 0.0 +11 6265569 exm884887 A T 0.0 0.0 0.0371 +11 6280138 JHU_11.6280137 G C 0.001 0.0 0.121 +11 6300368 JHU_11.6300367 G C 0.0 0.0 0.0189 +11 6301554 JHU_11.6301553 A T 0.9185 0.9802 0.8449 +11 6314569 rs7106875 T A 0.2604 0.2669 0.1339 +11 6317127 JHU_11.6317126 A T 0.0 0.0 0.0598 +11 6317590 JHU_11.6317589 G C 0.2286 0.1885 0.2534 +11 6318273 JHU_11.6318272 A T 0.1074 0.1012 0.2179 +11 6349526 rs118131016 A T 0.0249 0.0 0.0008 +11 6379270 rs10839557 G C 0.0746 0.0833 0.0809 +11 6385073 rs2255200 C G 0.7863 0.7966 0.4236 +11 6423375 exm2219099 G C 0.0 0.0 0.0 +11 6423375 rs201361208 G C 0.0 0.0 0.0 +11 6489719 rs56024253 G C 0.1292 0.0119 0.0091 +11 6519818 exm885543 G C 0.001 0.0 0.0 +11 6528934 JHU_11.6528933 A T 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16252086 ilmnseq_16:16252086 T A 0.001 0.0 0.1188 +16 16278869 kgp5026912 G C 0.4861 0.1627 0.3245 +16 16278869 rs8058696 G C 0.4861 0.1627 0.3245 +16 16291350 ilmnseq_16:16291350 C G 0.0 0.0 0.0106 +16 16291871 ilmnseq_16:16291871 G C 0.7386 0.9425 0.6687 +16 16906915 rs12919012 C G 0.0408 0.0129 0.0257 +16 16912158 rs4238664 C G 0.0169 0.0 0.1006 +16 16912644 JHU_16.16912643 T A 0.2485 0.121 0.0983 +16 16947660 rs8044389 T A 0.0 0.0 0.3094 +16 16976610 JHU_16.16976609 A T 0.0 0.0 0.112 +16 17025130 16:17025130-G-C C G 0.0 0.0 0.0 +16 17045116 JHU_16.17045115 T A 0.0 0.0 0.0416 +16 17107326 rs7204769 T A 0.7306 0.9415 0.879 +16 17139471 rs12446404 C G 0.2078 0.7014 0.0946 +16 17148828 rs76765951 A T 0.0239 0.0 0.0 +16 17179125 rs80112392 T A 0.0099 0.0099 0.1346 +16 17190126 rs61736029 A T 0.0 0.0367 0.0371 +16 17194235 JHU_16.17194234 T A 0.0815 0.0308 0.4841 +16 17211505 exm1220892 G C 0.0 0.0 0.0 +16 17211764 exm1220912 G C 0.0 0.0 0.0136 +16 17221308 rs4782035 A T 0.4245 0.1042 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48175156 kgp16367061 C G 0.0 0.005 0.0 +16 48201131 kgp4393797 C G 0.0765 0.0446 0.1309 +16 48204078 rs61739606 T A 0.0915 0.0 0.0779 +16 48234363 rs199774602 C G 0.001 0.0 0.0 +16 48235577 rs8050120 C G 0.1809 0.0437 0.3994 +16 48239193 ilmnseq_16:48239193 G C 0.0 0.0 0.0113 +16 48244904 exm1238616 G C 0.0 0.0 0.003 +16 48268295 JHU_16.48268294 T A 0.1014 0.0188 0.2458 +16 48284674 rs140666659 G C 0.0 0.0089 0.0 +16 48285266 rs141794561 C G 0.0 0.0407 0.0 +16 48373732 rs16946107 G C 0.0 0.0397 0.0 +16 48399361 exm1238837 G C 0.0 0.0 0.0242 +16 48411203 JHU_16.48411202 C G 0.0 0.0 0.0197 +16 48559172 rs77737484 G C 0.1859 0.0923 0.0045 +16 48646852 16:48646852-A-T A T 0.3221 0.2341 0.6014 +16 48651377 JHU_16.48651376 A T 0.3231 0.2431 0.584 +16 48753449 JHU_16.48753448 C G 0.0 0.0 0.0257 +16 48763623 rs62060317 C G 0.0368 0.0 0.0023 +16 48799978 rs140620148 G C 0.0 0.0188 0.0015 +16 48867969 JHU_16.48867968 G C 0.0964 0.0119 0.0136 +16 48960677 rs9929730 G C 0.0 0.0 0.0711 +16 48965085 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0.5716 0.8323 0.91 diff --git a/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/1000_Genomes_AF/PsychChip_15048346_B.1.3.1000_Genomes_AF.txt b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/1000_Genomes_AF/PsychChip_15048346_B.1.3.1000_Genomes_AF.txt new file mode 100644 index 0000000..eb6a3cb --- /dev/null +++ b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/1000_Genomes_AF/PsychChip_15048346_B.1.3.1000_Genomes_AF.txt @@ -0,0 +1,10808 @@ +chr position ID A1 A2 af_eur af_eas af_afr +1 889403 exm355 T A 0.0 0.0 0.0219 +1 892388 exm396 C G 0.0 0.0 0.0008 +1 907676 exm714 A T 0.0 0.0 0.0038 +1 909015 exm767 G C 0.0 0.0 0.0008 +1 979748 exm1081 A T 0.0467 0.0079 0.0008 +1 980863 exm1101 C G 0.0 0.0 0.0015 +1 1120370 exm1640 C G 0.0 0.0 0.1006 +1 1120377 exm1641 T A 0.0179 0.0 0.003 +1 1139251 exm1687 C G 0.0 0.0 0.0053 +1 1219382 exm2062 C G 0.0 0.0 0.0522 +1 1222279 exm2113 C G 0.0 0.0 0.0015 +1 1222528 exm2130 A T 0.002 0.0 0.0 +1 1223385 exm2183 G C 0.0229 0.6111 0.354 +1 1226797 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0.0 0.0 0.0083 +22 50356432 exm1620180 A T 0.0 0.0 0.0076 +22 50444043 psy_rs137854 C G 0.5179 0.5526 0.6203 +22 50530501 exm1620547 A T 0.2356 0.255 0.1301 +22 50632055 exm1620861 G C 0.0 0.0 0.0015 +22 50649223 exm1621006 G C 0.001 0.0 0.0 +22 50660214 exm2017001 C G 0.0 0.0 0.0 +22 50678739 exm2017060 T A 0.0 0.004 0.0 +22 50682361 exm2017067 C G 0.001 0.0 0.0 +22 50900141 exm1622741 G C 0.0 0.0 0.003 +22 50901349 exm1622791 C G 0.001 0.0 0.0008 +22 50903029 exm1622815 T A 0.0 0.0 0.0265 +22 50959456 exm2255274 C G 0.0 0.0 0.0113 +22 50962782 exm1623457 C G 0.6183 0.6677 0.6558 +22 51011376 exm1623703 G C 0.1143 0.501 0.6679 +22 51064039 exm1623987 G C 0.5288 0.3214 0.3578 +22 51065266 exm1624014 G C 0.0 0.0 0.0008 +22 51144513 exm2255280 C G 0.001 0.0 0.0015 diff --git a/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/README.md b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/README.md new file mode 100644 index 0000000..578efc4 --- /dev/null +++ b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/README.md @@ -0,0 +1,77 @@ +This subdirectory provides tools for assessing whether your PLINK format genotyping data is affected by the strand ambiguous bug, and for fixing the bug by flipping the designated alleles in the binary map (or .bim) file at each affected SNP. + +## Assessing Strand Ambiguous Bug +The shell script `compare_frequencies_against_1kg.r` can be used to determine if the bug has affected your data by plotting allele frequencies against 1000 genomes allele frequencies. The output of the script is a scatter plot, where the x-axis and y-axis are allele frequencies of your data and of 1000 genomes respectively. The subdirectory `1000_Genomes_AF subdirectory` contains 1000 genomes allele frequencies of strand ambiguous SNPs affected by the bug. + +- If your data has SNPs affected by the bug, you'll observe a negative slope (i.e. y=-x pattern) in your output plot (see `pre_flip.pdf`) +- If your data doesn't suffer strand ambiguous bug, you'll observe a positive slope (i.e. y=x pattern) in your output plot (see `post_flip.pdf`) + +**Invocations:** + +``` +usage: Rscript compare_frequencies_against_1kg.r \ + --frq \ + --frq1kg <1KG_FRK_FILE> \ + [--pop ] \ + [--out ] + + = allele frequencies calculated using `PLINK --freq` command. +<1KG_FRK_FILE> = allele frequencies of 1000 genomes from ./1000_Genomes_AF subdirectory + = population name choosing from EUR, EAS and AFR. default is EUR + = output plot name. default is `af.pdf` +``` + +To run this R script, package `dplyr`, `ggplot2` and `optparse` should be installed. + +**Examples:** + +You can calculate the allele frequencies of your genotypes file by running `plink --freq`. Remember to add `--keep-allele-order` to forces the original A1/A2 allele encoding to be preserved. Both [PLINK 1.07](http://zzz.bwh.harvard.edu/plink/) and [1.9](https://www.cog-genomics.org/plink2) support these commands. + +``` +plink --bfile --freq --keep-allele-order +``` + +Running the command above will generate a `plink.frq` file. Then you can evaluate whether or not your data is affected by running the command below. In this example, your data is of European ancestry, and the genotyping platform is GSAMD. If not output filename is specified, a `af.pdf` file whill be generated in the current directory. + +``` +Rscript compare_frequencies_against_1kg.r \ + --frq plink.frq \ + --frq1kg 1000_Genomes_AF/GSAMD-24v1-0_20011747_A1.1.3.1000_Genomes_AF.txt \ + --pop EUR +``` +Suppose your genotyping platform used is PsychChip_v1-1, the ancestry of your cohort is East Asian, and you want your output file to be named as `af_eas.pdf`. You should run: + +``` +Rscript compare_frequencies_against_1kg.r \ + --frq plink.frq \ + --frq1kg 1000_Genomes_AF/PsychChip_v1-1_15073391_A1.1.3.1000_Genomes_AF.txt \ + --pop EAS \ + --out af_eas.pdf +``` + + +## Flipping Affected SNPs +The python script `allele_flip.py` can take the PLINK .bim file and interval list file as inputs to flip the alleles of affected SNPs (i.e. swaps A↔T and C↔G alleles, but does not flip strand). In the absence of a specified log file, the log will be output to stdout. + +**Invocations:** + +``` +usage: flip_alleles.py [-h] --bim-in --bim-out --list + [--log LOG] + + = PLINK .bim file to be flipped += PLINK .bim with flipped alleles + = list of positions with affected SNPs from ../IntervalLists subdirectory +``` +To run this script, module `pandas` should be installed. The script can be run in either Python-2.7 or Python-3. + +**An Example log:** + +``` +python flip_alleles.py --list ../IntervalLists/GSAMD-24v1-0_20011747_A1.1.3.interval_list --bim-in --bim-out + +log output: +number of SNPs in interval list to flip alleles: [XXX] +number of SNPs successfully matched and alleles flipped in map file: [XXX] +updated map file is here: +``` diff --git a/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/compare_frequencies_against_1kg.r b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/compare_frequencies_against_1kg.r new file mode 100644 index 0000000..f5fe79b --- /dev/null +++ b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/compare_frequencies_against_1kg.r @@ -0,0 +1,65 @@ +library(dplyr) +library(ggplot2) +library(optparse) + + +# specify input parameters +option_list = list( + # input allele frequencies calculated using PLINK + make_option(c("--frq"), type="character", default=NULL, + help="path to PLINK .frq file", metavar="character"), + # 1000 Genomes allele frequencies + make_option(c("--frq1kg"), type="character", default=NULL, + help="path to 1000 Genomes allele freqeunecies", metavar="character"), + # continential ancestries, choosing between EUR, EAS and AFR + make_option(c("--pop"), type="character", default='EUR', + help="which superpopulation (choose from EUR, EAS, AFR)", metavar="character"), + # output plot path + make_option(c("--out"), type="character", default="af.pdf", + help="output file name [default= %default]", metavar="character") +); + +# make options +opt_parser = OptionParser(option_list=option_list); +opt = parse_args(opt_parser); + +# error check +if (! opt$pop %in% c("EUR", "EAS", "AFR")) {stop("The population can only be EUR, EAS and AFR!")} + +# import allele frq +cat("Start importing allele frequencies!\n") +# 1 rs113288277 T A 0.9609 486 +frq <- read.delim(opt$frq, sep='', header=TRUE, as.is=TRUE, + colClasses=c('character', 'character', 'character', 'character', 'numeric', 'numeric')) + +# import 1KG allele frequencies +cat("Starting importing allele frequencies of 1KG!\n") +# chr position ID A1 A2 af_eur af_eas af_afr +# 1 979748 rs113288277 A T 0.0467 0.0079 0.0008 +# 1 980824 seq-rs112039851 G C 0.003 0.0268 0.0726 +frq1kg <- read.delim(opt$frq1kg, sep='', header=TRUE, as.is=TRUE, + colClasses=c("character", "numeric", "character", "character", "character", "numeric", "numeric", "numeric")) +colnames(frq1kg) <- c("chr", "position", "SNP", "A1", "A2", "AF_EUR", "AF_EAS", "AF_AFR") + +# merge +n_tmp1 <- nrow(inner_join(frq, frq1kg, by = c("SNP" = "SNP", "A1" = "A2", "A2" = "A1"))) +n_tmp2 <- nrow(inner_join(frq, frq1kg, by = c("SNP" = "SNP", "A1" = "A1", "A2" = "A2"))) + +if (n_tmp1 > n_tmp2) { + frq <- frq %>% inner_join(frq1kg, by = c("SNP" = "SNP", "A1" = "A2", "A2" = "A1")) +} else { + frq <- frq %>% + inner_join(frq1kg, by = c("SNP" = "SNP", "A1" = "A1", "A2" = "A2")) %>% + mutate(MAF = 1 - MAF) +} + +# plot +p <- ggplot(frq, aes_string(x='MAF', y=paste0("AF_", opt$pop))) + + geom_point(color='red') + + xlab("Allele frequencies") + + ylab(paste0("Allele frequencies (1KG ", opt$pop, " )")) + + theme_bw() + +pdf(opt$out) +print(p) +dev.off() \ No newline at end of file diff --git a/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/flip_alleles.py b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/flip_alleles.py new file mode 100644 index 0000000..c4b726e --- /dev/null +++ b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/flip_alleles.py @@ -0,0 +1,72 @@ +#!/bin/python +import argparse +import pandas as pd + +def __main__(bim_in, bim_out, snps_list, log): + + # step 1: import bim data + bim_data = pd.read_csv(bim_in, + sep="\s+", + header=None, + names=["CHR", "RSID", "DIST (Morgan)", "DIST (BP)", "A1", "A2"], + dtype={'CHR': str, 'RSID': str, 'DIST (Morgan)': int, 'DIST (BP)': int, "A1": str, "A2": str}) + + # step 2: import SNPs list + snps = pd.read_csv(snps_list, sep='\s+', comment='@', + header=None, names=['CHR', 'START', 'END', 'STRAND', 'RSID']) + + # step 3: split multiple SNPs row + snps = snps['RSID'].str.split('|').apply(pd.Series, 1).stack() + snps.index = snps.index.droplevel(-1) + snps.name = 'RSID' + + # step 5: convert it to a list + snps = snps.tolist() + + # step 6: count number of SNPs in the list + n_snps = len(snps) + + # step 7: count number of SNPs matched + n_snps_matched = sum(bim_data['RSID'].isin(snps)) + + # step 8: flip alleles + tmp1 = bim_data.loc[bim_data['RSID'].isin(snps), 'A2'] + tmp2 = bim_data.loc[bim_data['RSID'].isin(snps), 'A1'] + bim_data.loc[bim_data['RSID'].isin(snps), 'A1'] = tmp1 + bim_data.loc[bim_data['RSID'].isin(snps), 'A2'] = tmp2 + + # step 9: export bim + bim_data.to_csv(bim_out, sep=' ', header=False, index=False) + + # step 10: save log_info to log if --log is specified, otherwise output log_info to stdout + log_info = 'python 08.-flip_alleles.py \n' \ + '--list %s \n' \ + '--bim-in %s \n' \ + '--bim-out %s \n\n' \ + 'log output: \n' \ + 'number of SNPs in interval list to flip alleles: %d\n' \ + 'number of SNPs successfully matched to map file: %d\n' \ + 'updated map file is here: %s\n'\ + 'Note that the first XXX should equal the second XXX if all went well.\n'% (snps_list, bim_in, bim_out, n_snps, n_snps_matched, bim_out) + + if log is None: + print(log_info) + else: + log_handler = open(log, 'w') + log_handler.write(log_info) + log_handler.close() + + +if __name__ == '__main__': + parser = argparse.ArgumentParser() + + parser.add_argument('--bim-in', action='store', dest='bim_in', required=True) + parser.add_argument('--bim-out', action='store', dest='bim_out', required=True) + parser.add_argument('--list', action='store', dest='snps_list', required=True) + parser.add_argument('--log', action='store', dest='log', required=False, default=None) + args = parser.parse_args() + + __main__(bim_in=args.bim_in, + bim_out=args.bim_out, + snps_list=args.snps_list, + log=args.log) \ No newline at end of file diff --git a/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/post_flip.pdf b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/post_flip.pdf new file mode 100644 index 0000000..b7270aa Binary files /dev/null and b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/post_flip.pdf differ diff --git a/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/pre_flip.pdf b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/pre_flip.pdf new file mode 100644 index 0000000..0fb96d1 Binary files /dev/null and b/ArraysAmbiguousSNPMiscallingMar2019/allele_flip/pre_flip.pdf differ