1 changed files with 3 additions and 1 deletions
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tasks/bcftools_concat.wdl
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| nt=$(nproc) | nt=$(nproc) | ||||
| bcftools concat -a ${vcf_indels} ${vcf_snvs} -Oz -o ${sample_id}_stralka.vcf.gz | bcftools concat -a ${vcf_indels} ${vcf_snvs} -Oz -o ${sample_id}_stralka.vcf.gz | ||||
| bcftools index -t ${sample_id}_stralka.vcf.gz | |||||
| >>> | >>> | ||||
| } | } | ||||
| output { | output { | ||||
| File norm_vcf = "${sample_id}_stralka.vcf.gz" | |||||
| File concat_vcf = "${sample_id}_stralka.vcf.gz" | |||||
| File concat_vcf_index = "${sample_id}_stralka.vcf.gz.tbi" | |||||
| } | } | ||||
| } | } |
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