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.

Running GATK on small pieces of a large BAM file

Hi Team,

I need to know something and hopefully is simple to implement. I have to run GATK HaplotypeCaller on a large BAM file, thus I have to run this in batches of 4 hours top. I've done some test to determine the appropriate size for the subsampled BAM. So let's say I need to run 10 jobs. Each one of those will output a gVCG file, which all belong to the same individual in this experiment.
I have read that there are several methods to parse and merge VCF files into a single one like CatVariants, CombineGVCFs and CombineVariants. The question is that I'm inclined to use CombineGVCFs since is the output I have, but I also have the understanding that this is for merging different individuals which is not what I have to do. So which approach should I use?
Thanks for the inputs!!!
Alejandro

Tagged:

Best Answer

Answers

Sign In or Register to comment.