#!/bin/bash -Ceuo pipefail
/opt/deepvariant/bin/run_deepvariant \
--ref=Homo_sapiens_assembly38.fasta \
--reads=Sig_18_Blood.recalibrated.bam \
--output_vcf=Sig_18_Blood.dv_rescue.vcf.gz \
--output_gvcf=Sig_18_Blood.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