.command.sh - Workdir - DAQ:CONTROL_VARIANT_CALLING:CONTROL_SOMATIC_VC:VCF_SOMATIC_SNV_INDEL:WHATSHAP (positive_somatic_control_1:chr18)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/e607d3c99220bc5475487ad625b55f/.command.sh
Size: 680 bytes
Task: DAQ:CONTROL_VARIANT_CALLING:CONTROL_SOMATIC_VC:VCF_SOMATIC_SNV_INDEL:WHATSHAP (positive_somatic_control_1:chr18)
Attempt

Content

#!/bin/bash -Ceuo pipefail
if [ -n "chr18" ]; then
    tabix -h positive_somatic_control_1.snv_indel.merged.vcf.gz chr18 > input_filtered.vcf
    bgzip input_filtered.vcf
    input_vcf="input_filtered.vcf.gz"
else
    input_vcf="positive_somatic_control_1.snv_indel.merged.vcf.gz"
fi

whatshap \
    phase \
     \
    --reference Homo_sapiens_assembly38.fasta \
    -o positive_somatic_control_1.snv_indel.whatshap.chr18.phased.vcf.gz \
    $input_vcf \
    FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.recalibrated.bam

cat <<-END_VERSIONS > versions.yml
"DAQ:CONTROL_VARIANT_CALLING:CONTROL_SOMATIC_VC:VCF_SOMATIC_SNV_INDEL:WHATSHAP":
    whatshap: $(whatshap --version)
END_VERSIONS