plink sex check not working - Error: --check-sex/--impute-sex requires at least one polymorphic X chromosome locus.

Question

[HrasteljJ]

Hi all,

I'm just starting my very first genotyping QC in plink and am trying to identify sex discordant individuals in my cohort.

I tried to run sex-check, and I get a return error message and it doesn't create a .sexcheck document:

594398 variants loaded from .bim file. 509 people (160 males, 349 females) loaded from .fam. Using 1 thread (no multithreaded calculations invoked. Before main variant filters, 509 founders and 0 nonfounders present. Calculating allele frequencies... done. Total genotyping rate is 0.997959. 594398 variants and 509 people pass filters and QC. Note: No phenotypes present. Error: --check-sex/--impute-sex requires at least one polymorphic X chromosome locus.

Does anyone know why this would be?

Thanks, James

[WouterDeCoster]

Please add information about where the data comes from and with which technology it was generated. Does your experiment cover the X chromosome?

Answer 1

[HrasteljJ]

Problem solved - it was the X chromosome labelling that was causing the problem.

[davidc]

Thanks that solved my problem - here's how I renamed the chromosomes:

bcftools annotate --rename-chrs chrs.map samples.vcf.gz | bgzip > samples_renamed.vcf.gz

where chrs.map is a text file with the old names mapped to the new names one per line space seperated e.g.: for Affymetrix Axiom

24 X
25 Y
26 MT

other arrays might have

23 X
24 Y
25 MT