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.
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?