Feature request: bam csi index support

[duceppemo]

I would like to use DeppVariant on organisms with chromosomes larger than 512Mbp. Currently, DeepVariant only supports .bai bam indexes.

[pichuan]

Thanks for the request. I can take a look.

[pichuan]

Hi @duceppemo , can you clarify what error message you were seeing when you try with a BAM file with .csi indices?

I just tested with data from https://github.com/google/deepvariant/blob/r1.2/docs/deepvariant-quick-start.md

And I deliberately deleted the .bai index file and created a .csi instead:

$ rm -f quickstart-testdata/NA12878_S1.chr20.10_10p1mb.bam.bai
$ samtools index -c quickstart-testdata/NA12878_S1.chr20.10_10p1mb.bam
$ ls quickstart-testdata/NA12878_S1.chr20.10_10p1mb.bam*
quickstart-testdata/NA12878_S1.chr20.10_10p1mb.bam
quickstart-testdata/NA12878_S1.chr20.10_10p1mb.bam.csi

After that, it seems like I was still able to go through the Quick Start steps without any issues.

DeepVariant is using htslib to read BAM files, and it seems like .csi is already supported there. Can you give me an reproducible example, if you're seeing any issues?

Thanks!

[duceppemo]

You are totally right! I should have tested it before creating an issue...

I also tested DeepVariant using cram and crai index files and it worked also. Maybe that information could be explicitly added to the documentation to prevent other (lazy) users to report same "issues".

Thanks a million!