Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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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