HaploType Caller(v3.3). Whole sample bam file vs per chromosome bam file


I am trying to call variants using HT caller (v3.3) in a human exome sample. I had to split the bam file into per chromosome bam files for faster processing. I did the realignment, print reads (after recalibration) steps at per chromsome level and base quality recalibration step at the sample level. Can I use HT caller to call variants per chromosme using per chromsome bam files as input or do I have to input all the chromsome bam files to the HT caller at once even though I want to call variants only on one chromosome at a time ?



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