File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/e6420e2d05b5fc1fc1969255e6afa6/.command.sh
Size
564 bytes
Task
VARIANT_COMPARISON_TSO500:BCFTOOLS_NORM_TEST (1029_1BK-T1-TDNA-1_B23KFCWLT4_1_vs_1029_1BK-N1-BDNA-1_B23KGCJLT4_1)
Attempt

Content

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#!/bin/bash -Ceuo pipefail
bcftools norm \
    -m-both \
    -a \
    -f Homo_sapiens_assembly38.fasta \
    --output-type v \
    1029_1BK-T1-TDNA-1_B23KFCWLT4_1_vs_1029_1BK-N1-BDNA-1_B23KGCJLT4_1.snv_indel.phased.vep.final.vcf.gz \
| bcftools norm \
    -m-both \
    --output-type z \
    --output 1029_1BK-T1-TDNA-1_B23KFCWLT4_1_vs_1029_1BK-N1-BDNA-1_B23KGCJLT4_1.norm.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