#!/bin/bash -Ceuo pipefail
/opt/deepvariant/bin/run_deepvariant \
    --ref=Homo_sapiens_assembly38.fasta \
    --reads=HCC1395_BL.recalibrated.bam \
    --output_vcf=HCC1395_BL.dv_rescue.vcf.gz \
    --output_gvcf=HCC1395_BL.dv_rescue.g.vcf.gz \
    --model_type=WES \
    --regions=germline_rescue_targets.bed \
     \
    --intermediate_results_dir=tmp \
    --num_shards=4

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DV_RESCUE":
    deepvariant: 1.6.1
END_VERSIONS