bam index file in .csi format

[akshaya-v]

Hello Whippet team!

I am trying to build a BAM supplemented index on Whippet. I used samtools to combine multiple bam files, remove duplicates, sort and index the bam file. Since the chromosomes are long, I had to use the .csi index option (-c) instead of the .bai index option (-b). However Whippet doesn't accept .csi index. Is there a way to fix this issue?

Thanks.

[timbitz]

Hi @akshaya-v -- Whippet uses XAM.jl to parse bam files, and csi isn't yet supported. I'm sure it will be at some point, but I don't have any immediate solution to fix this. The bai index has a max binsize that it seems your species' chromosomes exceed.

[akshaya-v]

Hello @timbitz, thank you very much for your response. Yes, I work on wheat in which about 10 chromosomes are longer than the Samtools bai index compatible length of 512 Mbp. For time being, I will use the 'annotation only index' on Whippet. Hope the complexities of plant genomes will be taken into consideration in future bioinformatics tools :)