1000 genomes missing SNPs on chr X in GRCh38

Question

[b_ha]

I am trying to get a reference together for imputation using the 1000 genomes data set. The GRCh38 version of the data set was made available earlier this year, but seems to be missing a significant number of SNPs on the X chromosome (~96%).

Is there any resource that can explain why? I have tried searching on their home page with no luck.

The data sets in question are GRCh38: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/

GRCh37: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/

[Emily]

Please do not cross post to BioStars, Stack Exchange and 1000 Genomes helpdesk as it can create duplicate work: https://bioinformatics.stackexchange.com/questions/10428/1000-genomes-missing-snps-on-chr-x-in-grch38

Answer 1

[Emily]

As I told you on 1000 genomes helpdesk:
Because of the ploidy settings we used for our variant calling, we only called variants in the the PARs on the X chromosome. We are working on settings to correctly analyse X variants in both males and females and plan to analyse X properly soon.