Working with sequences longer than 2^29-1

[Sagnik Banerjee]

Hello,

I work with Barley where most of the sequences are longer than 2^29-1. I have RNA-Seq data which map to regions beyond 2^29 on the chromosomes. I generally provide the .bam file to IGV. For this I need to generate the .bai file using samtools index. But this command fails since the there are regions which cannot be included in the bai index. Instead samtools recommends me to generate a .csi index file. IGV on the other hand cannot work with .csi index files. I am not sure how to use IGV for this. Any help will be appreciated.

Thank you.

[James Robinson]

Hi,  we rely on the htsjdk to load bam files.  They currently don't support the CSI index.    The place to request support is here:  https://github.com/samtools/htsjdk/issues.   When the htsjdk releases support for this we will update IGV to use it.

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