I am running an analysis in plink.

This is my first attempt at a QC and I keep encountering the same message when I try to go through with my sex check. I've done the SNP missingness step, it's this step that keeps stumping me. I'm assuming it has something to do with the chromosome naming but I'm a bit lost as to how I should tackle that problem. For reference, I attempted running the --check-sex function on the files (which are in bim, bed, fam) however, I'm met with this error.

431911 variants loaded from .bim file.
13635 people (7170 males, 6465 females) loaded from .fam.
13635 phenotype values loaded from .fam.
Using 1 thread (no multithreaded calculations invoked).
Before main variant filters, 13635 founders and 0 nonfounders present.
Calculating allele frequencies... done.
Total genotyping rate is 0.997824.
431911 variants and 13635 people pass filters and QC.
Among remaining phenotypes, 4457 are cases and 9178 are controls.
**Error: --check-sex/--impute-sex requires at least one polymorphic X chromosome

Does anybody know what I should do to fix this?

This is the command I used: plink --bfile ppmissingness2 --check-sex


1 Answer 1


Without X chromosome variation, sex cannot be reliably determined from input genotypes.

The error is telling you that there are no polymorphic X chromosome loci in the provided data. Either your input files don't include any X chromosome information (this could happen due to the increased statistical challenges involved in X chromosome data), or all the X chromosome "variants" are invariant / homozygous.


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