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bug

master
chaopower 2024-01-10 10:55:36 +08:00
parent def064acf4
commit 94b41eb45c
1 changed files with 1 additions and 1 deletions
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wdl/call_mutation.wdl
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@ -267,7 +267,7 @@ task mutation_calling_tissue_control {
vcf_add_tag_msi.pl ${output_dir}/mutation/${name}.raw.snp_indel.vcf ${output_dir}/mutation/${name}.raw.addtagmsi.snp_indel.vcf ${probe} t vcf_add_tag_msi.pl ${output_dir}/mutation/${name}.raw.snp_indel.vcf ${output_dir}/mutation/${name}.raw.addtagmsi.snp_indel.vcf ${probe} t
vcf_filter.py -i ${output_dir}/mutation/${name}.raw.addtagmsi.snp_indel.vcf \ vcf_filter.py -i ${output_dir}/mutation/${name}.raw.addtagmsi.snp_indel.vcf \
-o ${output_dir}/mutation/${name}.snp_indel.somatic.vcf -o ${output_dir}/mutation/${name}.snp_indel.somatic.vcf \
-e 'INFO/STATUS="StrongSomatic" | ( INFO/STATUS="LikelySomatic" && FORMAT/AF[0] > 3*FORMAT/AF[1] )' -e 'INFO/STATUS="StrongSomatic" | ( INFO/STATUS="LikelySomatic" && FORMAT/AF[0] > 3*FORMAT/AF[1] )'
vcf_filter.py -i ${output_dir}/mutation/${name}.raw.snp_indel.vcf \ vcf_filter.py -i ${output_dir}/mutation/${name}.raw.snp_indel.vcf \