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bug

master
chaopower 2024-01-15 13:29:24 +08:00
parent f09c61762c
commit ec9570521b
1 changed files with 3 additions and 3 deletions
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6
wdl/call_mutation.wdl
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@ -308,12 +308,12 @@ task hotspot {
-b $PUBLIC/hotspot/hotspot_delins.bed \ -b $PUBLIC/hotspot/hotspot_delins.bed \
-o ${output_dir}/mutation/${name}.raw.hotspot.delins.vcf -o ${output_dir}/mutation/${name}.raw.hotspot.delins.vcf
vcf_operations.py ${output_dir}/mutation/${name}.raw.hotspot.vcf \ vcf_operations.py ${raw_vcf} \
-b $PUBLIC/hotspot/hotspot_snpindel.bed \ -b $PUBLIC/hotspot/hotspot_snpindel.bed \
-o ${output_dir}/mutation/${name}.raw.hotspot.snpindel.vcf \ -o ${output_dir}/mutation/${name}.raw.hotspot.snpindel.vcf \
-s -s
vcf_operations.py ${output_dir}/mutation/${name}.raw.hotspot.vcf \ vcf_operations.py ${raw_vcf} \
-v $PUBLIC/hotspot/hotspot_snv.vcf \ -v $PUBLIC/hotspot/hotspot_snv.vcf \
-o ${output_dir}/mutation/${name}.raw.hotspot.snv.vcf -o ${output_dir}/mutation/${name}.raw.hotspot.snv.vcf
@ -455,7 +455,7 @@ task mutation_sum {
fi fi
{ head -n 1 ${somatic_txt} ; tail -n +2 ${somatic_txt} ; tail -n +2 ${hotspot_txt} ;} |\ { head -n 1 ${somatic_txt} ; tail -n +2 ${somatic_txt} ; tail -n +2 ${hotspot_txt} ;} |\
{ head -n 1 ; awk -F '\t' '{$1 = 1; OFS="\t" ; key=""; for (i=2; i<=NF-1; i++) { key = key $i "," } \ { head -n 1 ; awk -F '\t' '{$1 = 1; OFS="\t" ; key=""; for (i=3; i<=7; i++) { key = key $i "," } \
if (key in data) { data[key] = data[key] ";" $NF; } \ if (key in data) { data[key] = data[key] ";" $NF; } \
else { data[key] = $0; }} END { for (i in data) { print data[i]; } }' ; } > \ else { data[key] = $0; }} END { for (i in data) { print data[i]; } }' ; } > \
${output_dir}/mutation/${name}.snp_indel.somatic.hg19_multianno.filter.sum.txt ${output_dir}/mutation/${name}.snp_indel.somatic.hg19_multianno.filter.sum.txt