1 changed files with 3 additions and 1 deletions
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tasks/bcftools_concat.wdl
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| @@ -14,10 +14,12 @@ task bcftools { | |||
| set -e | |||
| nt=$(nproc) | |||
| bcftools concat -a ${vcf_indels} ${vcf_snvs} -Oz -o ${sample_id}.strelka.vcf.gz | |||
| bcftools concat -a ${vcf_indels} ${vcf_snvs} -Oz -o ${sample_id}.strelka.vcf.gz | |||
| bcftools norm -m -both ${sample_id}.strelka.vcf.gz -O z -o ${sample_id}.strelka.norm.vcf.gz | |||
| bcftools view -O z -f 'PASS' ${sample_id}.strelka.norm.vcf.gz -o ${sample_id}.strelka.PASS.vcf.gz | |||
| bcftools index -t ${sample_id}.strelka.PASS.vcf.gz | |||
| ls ./ | |||
| >>> | |||
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