Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

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.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!

When VQSR run using Whole genome sequencing data.

I ran GATK(version GATK3.4-46) using whole genome sequencing data of 60 samples.
Using bwa, I aligned my WGS data to human reference genome (GRCh 37) including autosome, X, Y, MT, and GL_****.
I ran HaplotypeCaller, and then using GenotypeGVCFs, VCF was extracted for chr1 - chr22, chrX, chrY.
I wonder what do mean WGS that GATK' Bestpractices recommend.
when GATK (VQSR, HC et al) was used,** to get the best result**, should WGS be consisted of autosome, X, Y, MT and GL_*****, ?
Or could it contain only the autosome excluding X ,Y?


Best Answer


Sign In or Register to comment.