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