Haplotypecaller batch mode

[bioinfor_worker]

when haplotypecaller runs in batch mode, it get errors, as below

singularity exec --nv clara-parabricks_4.0.1-1.sif pbrun haplotypecaller --batch --ref ref.fa --in-bam /data/bam/ --out-variants /date/gvcf/ --gvcf
Please visit NVIDIA Clara - NVIDIA Docs for detailed documentation

[E::hts_hopen] Failed to open file /data/bam/
[E::hts_open_format] Failed to open file “/data/bam/” : Is a directory
samtools view: failed to open “/data/bam/” for reading: Is a directory
[E::hts_hopen] Failed to open file /data/bam/
[E::hts_open_format] Failed to open file “/data/bam/” : Is a directory
samtools view: failed to open “/data/bam/” for reading: Is a directory
/usr/local/parabricks/binaries//bin/htvc /data/ref.fa /data/bam/ 2 -o /data/gvcf -nt 5
[PB Info 2023-Jul-03 00:37:15] ------------------------------------------------------------------------------
[PB Info 2023-Jul-03 00:37:15] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2023-Jul-03 00:37:15] || Version 4.0.1-1 ||
[PB Info 2023-Jul-03 00:37:15] || GPU-GATK4 HaplotypeCaller ||
[PB Info 2023-Jul-03 00:37:15] ------------------------------------------------------------------------------
[PB Error 2023-Jul-03 00:37:15][src/haplotype_vc.cpp:854] Expected file “/data/bam/” to be of type bam, cram or text, exiting.

[mdemouth]

Hi @bioinfor_worker ,

sorry but --batch is deprecated. The documentation was not updated.

If you would like to run on a batch style you can however.
You will need to create two files, one with the list of paths to your bam files (for example, bamList.txt) and one with the path to the generated vcf files (for example vcfList.txt).

You can run with :
pbrun haplotypecaller --ref ref.fa --in-bam bamList.txt --out-variants vcfList.txt

Please let us know if you have any issue.