Major sex differences in allele frequencies for X chromosomal variants in both the 1000 Genomes Project and gnomAD
Zhong Wang, Lei Sun, Andrew D. Paterson
2022
PLoS Genet 18(5): e1010231. https://doi.org/10.1371/journal.pgen.1010231
- The Genome Reference Consortium: https://www.ncbi.nlm.nih.gov/grc/human
- The 1000 Genomes Project: https://www.internationalgenome.org
- Phase 3 data of the 1000 Genomes Project: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ and the specific vcf file used: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chrX.phase3_shapeit2_mvncall_integrated_v1b.20130502.genotypes.vcf.gz
- High coverage phased data of the 1000 Genomes Project: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20201028_3202_phased/CCDG_14151_B01_GRM_WGS_2020-08-05_chrX.filtered.eagle2-phased.v2.vcf.gz
- gnomAD v.3.1.2 allele counts from genome sequence: https://gnomad.broadinstitute.org/downloads
- chrX sites VCF: 95.6 GiB, MD5: 040080a18046533728fa60800eedcf4b
- gnomAD v.2.1 structural variants: (https://gnomad.broadinstitute.org/gene/ENSG00000124343?dataset=gnomad_sv_r2_1)