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Allele flip (#5)
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* adding allele_flip folder
* adding 1000 Genomes AF of affected variants
* adding notes for allele_flip to README.md
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@danfengc
danfengc authored and Yossi Farjoun committed Mar 27, 2019
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3 changes: 2 additions & 1 deletion ArraysAmbiguousSNPMiscallingMar2019/README.md
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Expand Up @@ -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.
194 changes: 194 additions & 0 deletions ...9/allele_flip/1000_Genomes_AF/Broad_GWAS_supplemental_15061359_A1.1.3.1000_Genomes_AF.txt
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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
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