.command.sh - Workdir - VARIANT_COMPARISON_TSO500:FILTER_STAR_ALLELES_TRUTH (1029_8AV)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/7fe65eee87dbbd22bd89d11b1ce9e0/.command.sh
Size: 508 bytes
Task: VARIANT_COMPARISON_TSO500:FILTER_STAR_ALLELES_TRUTH (1029_8AV)
Attempt

Content

#!/bin/bash -Ceuo pipefail
bcftools view -e 'ALT="*"' --output-type z --output 1029_8AV.filtered.vcf.gz 1029_8AV.norm.vcf.gz
bcftools view -i 'ALT="*"' --output-type z --output 1029_8AV.star_alleles.vcf.gz 1029_8AV.norm.vcf.gz
bcftools index -t 1029_8AV.filtered.vcf.gz
bcftools index -t 1029_8AV.star_alleles.vcf.gz

cat <<-END_VERSIONS > versions.yml
"VARIANT_COMPARISON_TSO500:FILTER_STAR_ALLELES_TRUTH":
    bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*$//')
END_VERSIONS