Since samtools 1.0, csi indexing format of bam file is specifically used for any other organisms with long chromosomes ( > 536Mb). Could you help me figure out how to let GATK SplitNCigarReads support cis indexing file?
Thanks so much.
Unfortunately, we do not yet support csi.
Hopefully in the future we will though!
could you add this as an official feature request please?
I just checked the issue tracker page and can't find it on there (and it didn't look like there was an option for me to file a feature request myself).
We too deal with larger-than-human chromosomes and have a real need for this.
Hi @mb47, this is actually something that would have to be implemented in htsjdk, not GATK. You can file an issue here: https://github.com/samtools/htsjdk/issues
Hi there, I am using sambamba to create .bai indexes for larger-than-human chroms
Thank you so much for letting us know about sambamba!!!!