On can split a Split Bam Files By Region For Parallel Variant Calling to speed up the processing of the BAMs.
But it cannot be so simple: if two reads have been mapped on two distinct chromosomes, I'm afraid some operations could lose some informations about the pair. So I suppose, I should create one extra bam file to save those pairs
In the following operations what are the places where we can safely work on a given chromosome:
- GATK: Indel Realignment
- GATK recalibration
do you have any experience with splitting the bams ? is it worth it ?