Dear colleague,
I am interested in a number of columns in the file "HGDP + 1KG callset
- Genomes - Sample metadata TSV" downloaded from the link
(https://storage.googleapis.com/gcp-public-data--gnomad/release/3.1.2/vcf/genomes/gnomad.genomes.v3.1.2.hgdp_1kg_subset_sample_meta.tsv.bgz).
chr20_mean_dp: Sample’s mean depth across chromosome 20.
chrX_mean_dp: Sample’s mean depth across chromosome X.
chrY_mean_dp: Sample’s mean depth across chromosome Y.
I was wondering if you could help me understand how chr20_mean_dp,
chrX_mean_dp and chrY_mean_dp were calculated please? Is the Samtools
used for this calculation and what parameters are used?
For chrY_mean_dp, is “the whole chromosome Y” or “only the
male-specific region of the Y chromosome” used for the calculation?
For chrX_mean_dp, is “the whole chromosome X” or “only the region that
are unique to chromosome X” are used for the calculation?
Many thanks,
Best wishes,
Tom