.command.sh - Workdir - VARIANT_COMPARISON_TSO500:BCFTOOLS_NORM_TEST (1029_2LI-T1-TDNA-1_23K7YCLT4_1_vs_1029_2LI-N1-BDNA-1_235YY7LT3_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/eaa0df4668988ead650431451bf16a/.command.sh
Size: 467 bytes
Task: VARIANT_COMPARISON_TSO500:BCFTOOLS_NORM_TEST (1029_2LI-T1-TDNA-1_23K7YCLT4_1_vs_1029_2LI-N1-BDNA-1_235YY7LT3_1)
Attempt

Content

#!/bin/bash -Ceuo pipefail
bcftools norm \
    -m-both \
    -a \
    --output-type z \
    --output 1029_2LI-T1-TDNA-1_23K7YCLT4_1_vs_1029_2LI-N1-BDNA-1_235YY7LT3_1.norm.vcf.gz \
    1029_2LI-T1-TDNA-1_23K7YCLT4_1_vs_1029_2LI-N1-BDNA-1_235YY7LT3_1.snv_indel.phased.vep.final.vcf.gz

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