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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?


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