File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/c8a9cb57b46d5de611d231020a50b6/.command.sh
Size
564 bytes
Task
VARIANT_COMPARISON_TSO500:BCFTOOLS_NORM_TEST (1029_7ZM-T1-TDNA-1_A23MHVGLT4_1_vs_1029_7ZM-N1-BDNA-1_B23L5TMLT4_1)
Attempt

Content

View in new tab 
#!/bin/bash -Ceuo pipefail
bcftools norm \
    -m-both \
    -a \
    -f Homo_sapiens_assembly38.fasta \
    --output-type v \
    1029_7ZM-T1-TDNA-1_A23MHVGLT4_1_vs_1029_7ZM-N1-BDNA-1_B23L5TMLT4_1.snv_indel.phased.vep.final.vcf.gz \
| bcftools norm \
    -m-both \
    --output-type z \
    --output 1029_7ZM-T1-TDNA-1_A23MHVGLT4_1_vs_1029_7ZM-N1-BDNA-1_B23L5TMLT4_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