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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.
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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?