GATK variant calling for RNAseq data between groups

Question

[cpad0112]

Hi All

I am trying to construct a example workflow for RNA seq data analysis for variant calling. I am following this guide: https://www.broadinstitute.org/gatk/guide/article?id=3891 for variant calling. RNA seq data is obtained from here: https://test.galaxyproject.org/library_common/browse_library?show_deleted=False&cntrller=library&use_panels=False&id=d1d508fb296552d5.

To give you the gist, data has two groups labeled, MeOH and R3G with 3 replicates each and each replicate is sequenced paired-end. I was able to reproduce entire workflow (till calling variants for each replicate). I combined replicate vcfs for each group. I do not know how to compare between groups (here MeOH vs R3G). Currently, I hold two VCFs (one each for two groups: MeOH.vcf and R3G.vcf). Is there a way to compare between groups in GATK ? or do I have to use external tools to compare two VCFs?

[GouthamAtla]

http://vcftools.sourceforge.net/perl_module.html#vcf-compare