-
Notifications
You must be signed in to change notification settings - Fork 15
/
Copy pathmake_vc.sh
executable file
·221 lines (179 loc) · 8.96 KB
/
make_vc.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
#!/usr/bin/env bash
readonly DIR_SCRIPT=$(
cd "$(dirname "${BASH_SOURCE[0]}")" || exit 1
pwd -P
)
## load settings
# shellcheck source=common.cfg.sh
. "${DIR_SCRIPT}"/common.cfg.sh
function usage() {
echo "usage: miracum_pipe.sh -d dir [-h]"
echo " -d dir specify relative folder of patient"
echo " -p computing as parallel process"
echo " -h show this help screen"
exit 1
}
while getopts d:t:ph option; do
case "${option}" in
d) readonly PARAM_DIR_PATIENT=$OPTARG ;;
h) usage ;;
p) readonly PARALLEL_PROCESSES=2 ;;
\?)
echo "Unknown option: -$OPTARG" >&2
exit 1
;;
:)
echo "Missing option argument for -$OPTARG" >&2
exit 1
;;
*)
echo "Unimplemented option: -$OPTARG" >&2
exit 1
;;
esac
done
# if no patient is defined
if [[ -z "${PARAM_DIR_PATIENT}" ]]; then
echo "no patient defined."
echo "--"
usage
fi
# load patient yaml
readonly CFG_SEX=$(get_config_value sex "${PARAM_DIR_PATIENT}")
if [[ "$(get_config_value common.germline "${PARAM_DIR_PATIENT}")" = "True" ]]; then
readonly CFG_CASE=somaticGermline
else
readonly CFG_CASE=somatic
fi
# check inputs
readonly VALID_SEXES=("XX XY")
if [[ ! " ${VALID_SEXES[@]} " =~ " ${CFG_SEX} " ]]; then
echo "unknown sex: ${CFG_SEX}"
echo "use one of the following values: $(join_by ' ' ${VALID_SEXES})"
exit 1
fi
##################################################################################################################
## load programs
# shellcheck source=programs.cfg.sh
. "${DIR_SCRIPT}/programs.cfg.sh"
##################################################################################################################
[[ -d "${DIR_ANALYSES}" ]] || mkdir -p "${DIR_ANALYSES}"
# names
readonly NameD=${CFG_CASE}_${PARAM_DIR_PATIENT}_vc
readonly NameGD=${CFG_CASE}_${PARAM_DIR_PATIENT}_gd
readonly NameTD=${CFG_CASE}_${PARAM_DIR_PATIENT}_td
# input
readonly recalbamGD=${DIR_WES}/${NameGD}_output.sort.filtered.rmdup.realigned.fixed.recal.bam
readonly recalbamTD=${DIR_WES}/${NameTD}_output.sort.filtered.rmdup.realigned.fixed.recal.bam
# keep
readonly snpvcf=${DIR_WES}/${NameD}.output.snp.vcf
readonly indelvcf=${DIR_WES}/${NameD}.output.indel.vcf
readonly MSI_OUTPUT=${DIR_WES}/${NameD}_MSI
${BIN_MPILEUP} --adjust-MQ "${CFG_SAMTOOLS_MPILEUP_ADJUSTMQ}" --min-MQ "${CFG_SAMTOOLS_MPILEUP_MINMQ}" --min-BQ "${CFG_GENERAL_MINBASEQUAL}" --max-depth "${CFG_SAMTOOLS_MPILEUP_MAXDEPTH}" -f "${FILE_GENOME}" -l "${CFG_REFERENCE_CAPTUREREGIONS}" "${recalbamGD}" "${recalbamTD}" | ${BIN_SOMATIC} --output-snp "${snpvcf}" --output-indel "${indelvcf}" \
--min-coverage "${CFG_VARSCAN_SOMATIC_MINCOVERAGE}" --tumor-purity "${CFG_VARSCAN_SOMATIC_TUMORPURITY}" \
--min-var-freq "${CFG_GENERAL_MINVAF}" --min-freq-for-hom "${CFG_VARSCAN_SOMATIC_MINFREQFORHOM}" \
--min-avg-qual "${CFG_GENERAL_MINBASEQUAL}" --normal-purity "${CFG_VARSCAN_SOMATIC_NORMALPURITY}" \
--min-coverage-normal "${CFG_VARSCAN_SOMATIC_MINCOVERAGENORMAL}" --min-coverage-tumor "${CFG_VARSCAN_SOMATIC_MINCOVERAGETUMOR}" \
--p-value "${CFG_VARSCAN_SOMATIC_PVALUE}" --somatic-p-value "${CFG_VARSCAN_SOMATIC_SOMATICPVALUE}" \
--strand-filter "${CFG_VARSCAN_SOMATIC_STRANDFILTER}" --validation "${CFG_VARSCAN_SOMATIC_VALIDATION}" --output-vcf 1 --mpileup 1
# Processing of somatic mutations
${BIN_PROCESSSOMATIC} "${snpvcf}" --min-tumor-freq "${CFG_GENERAL_MINVAF}" \
--max-normal-freq "${CFG_VARSCAN_PROCESSSOMATIC_MAXNORMALFREQ}" --p-value "${CFG_VARSCAN_PROCESSSOMATIC_PVALUE}"
${BIN_PROCESSSOMATIC} "${indelvcf}" --min-tumor-freq "${CFG_GENERAL_MINVAF}" \
--max-normal-freq "${CFG_VARSCAN_PROCESSSOMATIC_MAXNORMALFREQ}" --p-value "${CFG_VARSCAN_PROCESSSOMATIC_PVALUE}"
# FP Filter: snp.Somatic.hc snp.LOH.hc snp.Germline.hc
# FP Filter: indel.Somatic.hc indel.LOH.hc indel.Germline.hc
readonly names1="snp indel"
for name1 in ${names1}; do
if [[ "${CFG_CASE}" = somatic ]]; then
names2="Somatic LOH"
else
names2="Somatic LOH Germline"
fi
for name2 in ${names2}; do
# temp
hc_avi=${DIR_WES}/${NameD}.output.${name1}.${name2}.hc.avinput
hc_rci=${DIR_WES}/${NameD}.output.${name1}.${name2}.hc.readcount.input
hc_rcs=${DIR_WES}/${NameD}.output.${name1}.${name2}.hc.readcounts
# keep
hc_vcf=${DIR_WES}/${NameD}.output.${name1}.${name2}.hc.vcf
hc_fpf=${DIR_WES}/${NameD}.output.${name1}.${name2}.hc.fpfilter.vcf
if [[ "${name2}" = "Somatic" ]]; then
recalbam=${recalbamTD}
else
recalbam=${recalbamGD}
fi
${CONVERT2ANNOVAR2} "${hc_avi}" "${hc_vcf}"
${BIN_CUT} "${hc_avi}" > "${hc_rci}"
${BIN_BAM_READCOUNT} -l "${hc_rci}" "${recalbam}" > "${hc_rcs}"
${BIN_VAR_SCAN} fpfilter "${hc_vcf}" "${hc_rcs}" --output-file "${hc_fpf}" --keep-failures 1 \
--min-ref-basequal "${CFG_GENERAL_MINBASEQUAL}" --min-var-basequal "${CFG_GENERAL_MINBASEQUAL}" \
--min-var-count "${CFG_VARSCAN_FPFILTER_MINVARCOUNT}" --min-var-freq "${CFG_GENERAL_MINVAF}" \
--min-var-count-lc "${CFG_VARSCAN_FPFILTER_MINVARCOUNTLC}" --max-somatic-p "${CFG_VARSCAN_FPFILTER_MAXSOMATICP}" \
--max-somatic-p-depth "${CFG_VARSCAN_FPFILTER_MAXSOMATICPDEPTH}" --min-ref-readpos "${CFG_VARSCAN_FPFILTER_MINREFREADPOS}" \
--min-var-readpos "${CFG_VARSCAN_FPFILTER_MINVARREADPOS}" --min-ref-dist3 "${CFG_VARSCAN_FPFILTER_MINREFDIST3}" \
--min-var-dist3 "${CFG_VARSCAN_FPFILTER_MINVARDIST3}" --min-strandedness "${CFG_VARSCAN_FPFILTER_MINSTRANDEDNESS}" \
--min-strand-reads "${CFG_VARSCAN_FPFILTER_MINSTRANDREADS}" --max-basequal-diff "${CFG_VARSCAN_FPFILTER_MAXBASEQUALDIFF}" \
--min-ref-avgrl "${CFG_VARSCAN_FPFILTER_MINREFAVGRL}" --min-var-avgrl "${CFG_VARSCAN_FPFILTER_MINVARAVGRL}" \
--max-rl-diff "${CFG_VARSCAN_FPFILTER_MAXRLDIFF}" --max-ref-mmqs "${CFG_VARSCAN_FPFILTER_MAXREFMMQS}" \
--max-var-mmqs "${CFG_VARSCAN_FPFILTER_MAXVARMMQS}" --min-mmqs-diff "${CFG_VARSCAN_FPFILTER_MINMMQSDIFF}" \
--max-mmqs-diff "${CFG_VARSCAN_FPFILTER_MAXMMQSDIFF}" --min-ref-mapqual "${CFG_VARSCAN_FPFILTER_MINREFMAPQUAL}" \
--min-var-mapqual "${CFG_VARSCAN_FPFILTER_MINVARMAPQUAL}" --max-mapqual-diff "${CFG_VARSCAN_FPFILTER_MAXMAPQUALDIFF}"
done
done
readonly data=${DIR_WES}
for name1 in ${names1}; do
# Annotation snp.Somatic.hc $data/NameD.output.snp.Somatic.hc.fpfilter.vcf
# Annotation indel.Somatic.hc $data/NameD.output.indel.Somatic.hc.fpfilter.vcf
# temp
hc=${DIR_WES}/${NameD}.output.${name1}.Somatic.hc
hc_T_avi=${DIR_WES}/${NameD}.output.${name1}.Somatic.hc.TUMOR.avinput
# keep
hc_fpf=${DIR_WES}/${NameD}.output.${name1}.Somatic.hc.fpfilter.vcf
hc_T_avi_multi=${DIR_WES}/${NameD}.output.${name1}.Somatic.hc.TUMOR.avinput.hg19_multianno.csv
hc_snpeff="${DIR_WES}/${NameD}.output.${name1}.Somatic.SnpEff.vcf"
# annovar annotation
${CONVERT2ANNOVAR} "${hc}" "${hc_fpf}" -allsample
${TABLEANNOVAR} "${hc_T_avi}" "${DIR_ANNOVAR_DATA}" -protocol "${CFG_ANNOVAR_PROTOCOL}" -buildver hg19 \
-operation "${CFG_ANNOVAR_ARGOP}" -csvout -otherinfo -remove -nastring NA
# snpEff; identify canonical transcript
${BIN_SNPEFF} "${hc_fpf}" > "${hc_snpeff}"
if [[ "${CFG_CASE}" = somaticGermline ]]; then
# Annotation snp.Germline.hc $data/NameD.output.snp.Germline.hc.fpfilter.vcf
# Annotation indel.Germline.hc $data/NameD.output.indel.Germline.hc.fpfilter.vcf
# temp
hc=${DIR_WES}/${NameD}.output.${name1}.Germline.hc
hc_N_avi=${DIR_WES}/${NameD}.output.${name1}.Germline.hc.NORMAL.avinput
# keep
hc_fpf=${DIR_WES}/${NameD}.output.${name1}.Germline.hc.fpfilter.vcf
hc_N_avi_multi=${DIR_WES}/${NameD}.output.${name1}.Germline.hc.NORMAL.avinput.hg19_multianno.csv
hc_N_snpeff=${DIR_WES}/${NameD}.output.${name1}.NORMAL.SnpEff.vcf
# annovar annotation
${CONVERT2ANNOVAR} "${hc}" "${hc_fpf}" -allsample
${TABLEANNOVAR} "${hc_N_avi}" "${DIR_ANNOVAR_DATA}" -protocol "${CFG_ANNOVAR_PROTOCOL}" -buildver hg19 \
-operation "${CFG_ANNOVAR_ARGOP}" -csvout -otherinfo -remove -nastring NA
# snpEff; identify canonical transcripts
${BIN_SNPEFF} "${hc_fpf}" > "${hc_N_snpeff}"
fi
# Annotation snp.LOH.hc
# Annotation indel.LOH.hc
# temp
hc_avi=${DIR_WES}/${NameD}.output.${name1}.LOH.hc.avinput
# keep
hc_fpf=${DIR_WES}/${NameD}.output.${name1}.LOH.hc.fpfilter.vcf
hc_avi_multi=${DIR_WES}/${NameD}.output.${name1}.LOH.hc.avinput.hg19_multianno.csv
hc_L_snpeff=${DIR_WES}/${NameD}.output.${name1}.LOH.SnpEff.vcf
# annovar annotation
${CONVERT2ANNOVAR3} "${hc_avi}" "${hc_fpf}"
${TABLEANNOVAR} "${hc_avi}" "${DIR_ANNOVAR_DATA}" -protocol "${CFG_ANNOVAR_PROTOCOL}" -buildver hg19 \
-operation "${CFG_ANNOVAR_ARGOP}" -csvout -otherinfo -remove -nastring NA
# snpEff; identify canonical transcript
${BIN_SNPEFF} "${hc_fpf}" > "${hc_L_snpeff}"
done
# MSI
if [ ! -f "${MICROSATELLITE_SITES}" ]; then
echo "${MICROSATELLITE_SITES} does not exist. Generating ..."
${MSISENSOR_PRO_SCAN} -d "${FILE_GENOME}" -o "${MICROSATELLITE_SITES}"
fi
${MSISENSOR_PRO} -d ${MICROSATELLITE_SITES} -n "${recalbamGD}" -t "${recalbamTD}" -o "${MSI_OUTPUT}"
#eo VC