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.
Problem with GATK pipeline, merging VCF and ped file.
Hi to all
I have just started using GATK and I have few question about some tools and about the general workflow.
I have 3 exome-seq data from a trio and I have to detect rare or private variants that segregate with the disease.
From the 3 aligned bam file I procedeed with the GATK pipeline (ADDgroupInfo, MarkDup, Realign, BQSR, Unified Genotyper and variant filtration) and I generated 3 VCF file.
As now I have to use the PhaseByTrasmission tool, should I merge the 3 VCF file?
Or it was better to merge the BAM file after adding the group info and proceed with the other analysis?
And should I create my .ped file,(I visited http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped, but I couln't understand how ped file is generated) based on the read group that I have assigned?