Dear,
This is my first post so please be tolerant, I am trying to issue a parabricks deepvariant_germline command including the parameter –haploid-contigs “chrX,chrY” but I get and error back.
Using the latest clara image (converted to singularity from a fresh docker) and the image works apparently for other commands but not when I include the parameter (present in the doc: deepvariant_germline - NVIDIA Docs)
I tried to double-quote, single-quote and escape both, no success !
thanks for your help
singimg="clara-parabricks_4.1.0-1.sif"
singularity run --nv \
> --bind "${WORK_DIR}:/workdir" \
> --bind "${TMPDIR}:/tmp" \
> --pwd "/workdir" \
> ${singimg} \
> pbrun deepvariant_germline \
> --gpusort \
> --gpuwrite \
> --num-gpus ${numgpu} \
> --bwa-options '-M -K 10000000' \
> --optical-duplicate-pixel-distance "${optdist}" \
> --read-group-sm "${pfx}" \
> --read-group-lb "lib_${pfx}" \
> --read-group-pl "${platform}" \
> --read-group-id-prefix "${pfx}" \
> --ref "/workdir/bwaidx/${refidx}" \
> --in-fq "/workdir/reads_chr20/${fq1}" "/workdir/reads_chr20/${fq2}" \
> --haploid-contigs \'X,Y\' \
> --knownSites "/workdir/reference/${knownsites}" \
> --out-bam "/workdir/${outbam}/${pfx}_mrkdup.bam" \
> --out-recal-file "/workdir/${outbam}/${pfx}_recal.txt" \
> --out-duplicate-metrics "/workdir/${outbam}/${pfx}_duplicate_metrics" \
> --out-variants "/workdir/variants/${pfx}.g.vcf.gz" \
> --gvcf \
> --tmp-dir "/tmp" \
> --logfile "/workdir/${outbam}/${pfx}_deepvariant_germline-log.txt"
Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation
usage: pbrun deepvariant_germline <options>
Help: pbrun deepvariant_germline -h
pbrun: error: unrecognized arguments: --haploid-contigs