Since our chromosomes are too large, could you please add support for the CSI index in the next update?
Here are the details of the issue: When I use pbrun haplotypecaller, despite having already built a CSI index for my BAM file, the program encountered an error when processing the position [PB Info 2025-Oct-29 06:34:50] Chr1:534240001 35.8 4129169 115232. The error message is as follows:
TEXT
E::hts_idx_push] Region 536870911..536870917 cannot be stored in a tbi index. Try using a csi index with min_shift = 14, n_lvls >= 6
[PB Error 2025-Oct-29 06:34:54][src/PBBgzfFile.cpp:608] Failure in hts_idx_push: -1, expected htsSts == 0, exiting.
/usr/local/parabricks/binaries/bin/htvc /workspace/Chr1.fa /workspace/ZWY_1_clean.sorted.Chr1.dedup.filtered.bam 1 -o /workspace/sample.Chr1.g.vcf.gz -nt 5 -g
Process exited with failure. Please check the logs.
Process exited with failure. Please check the logs.
For technical support visit NVIDIA Clara - NVIDIA Docs
Exiting…
Please visit NVIDIA Clara - NVIDIA Docs for detailed documentation
Could not run haplotypecaller
Exiting pbrun …
Here are the details of the issue: When I use pbrun haplotypecaller, despite having already built a CSI index for my BAM file, the program encountered an error when processing the position [PB Info 2025-Oct-29 06:34:50] Chr1:534240001 35.8 4129169 115232. The error message is as follows:
TEXT
E::hts_idx_push] Region 536870911..536870917 cannot be stored in a tbi index. Try using a csi index with min_shift = 14, n_lvls >= 6
[PB Error 2025-Oct-29 06:34:54][src/PBBgzfFile.cpp:608] Failure in hts_idx_push: -1, expected htsSts == 0, exiting.
/usr/local/parabricks/binaries/bin/htvc /workspace/Chr1.fa /workspace/ZWY_1_clean.sorted.Chr1.dedup.filtered.bam 1 -o /workspace/sample.Chr1.g.vcf.gz -nt 5 -g
Process exited with failure. Please check the logs.
Process exited with failure. Please check the logs.
For technical support visit https://docs.nvidia.com/clara/index.html#parabricks
Exiting...
Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation
Could not run haplotypecaller
Exiting pbrun ...
Is there a solution to this problem? Many thanks to the developers for their tools and assistance!