Workflow using HaplotypeCaller, GenotypeGVCFs, VQSR, and CalculateGenotypePosteriors

astrand

Hi,

I have recal.bam files for all the individuals in my study (these constitute 4 families), and each bam file contains information for one chromosome for one individual. I was wondering if it is best for me to pass all the files for a single individual together when running HaplotypeCaller, if it will increase the accuracy of the calling, or if I can just run HaplotypeCaller on each individual bam file separately.

Also, I was wondering at which step I should be using CalculateGenotypePosteriors, and if it will clean up the calls substantially. VQSR already filters the calls, but I was reading that CalculateGenotypePosteriors actually takes pedigree files, which would be useful in my case. Should I try to use CalculateGenotypePosteriors after VQSR? Are there other relevant filtering or clean-up tools that I should be aware of?

Thanks very much in advance,

Alva

Sheila

@astrand‌

Hi Alva,

You can either run HaplotypeCaller on each bam file separately or on all the bam files for each individual. The accuracy will not be affected.

This article should help to answer your other questions: http://gatkforums.broadinstitute.org/discussion/4723/genotype-refinement-workflow

-Sheila

Sheila

@astrand‌

Hi Alva,

You can either run HaplotypeCaller on each bam file separately or on all the bam files for each individual. The accuracy will not be affected.

This article should help to answer your other questions: http://gatkforums.broadinstitute.org/discussion/4723/genotype-refinement-workflow

-Sheila

astrand

Thanks for the information.

Alva