.command.sh - Workdir - VARIANT_COMPARISON_TSO500:BCFTOOLS_NORM_TEST (1029_7Y1-T1-TDNA-1_23FC2GLT4_s16_vs_1029_7Y1-N1-BDNA-1_2375WFLT3_s16)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/e2d4eda65b9bf699de126af87bf735/.command.sh
Size: 475 bytes
Task: VARIANT_COMPARISON_TSO500:BCFTOOLS_NORM_TEST (1029_7Y1-T1-TDNA-1_23FC2GLT4_s16_vs_1029_7Y1-N1-BDNA-1_2375WFLT3_s16)
Attempt

Content

#!/bin/bash -Ceuo pipefail
bcftools norm \
    -m-both \
    -a \
    --output-type z \
    --output 1029_7Y1-T1-TDNA-1_23FC2GLT4_s16_vs_1029_7Y1-N1-BDNA-1_2375WFLT3_s16.norm.vcf.gz \
    1029_7Y1-T1-TDNA-1_23FC2GLT4_s16_vs_1029_7Y1-N1-BDNA-1_2375WFLT3_s16.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