Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

GATK-Snp calling

JayceJayce Posts: 7Member

hi,

can anyone help to advice if splitting the bam files Versus splitting the -L region, which one could speed up faster? asssume that i have 500 bam files, will splitting the bam files to 22 different chromosomes will increase the speed further as compare to splitting the -L region (intervals)? Can anyone help to advice or probably had experienced it before. thank you.

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