X chromosome male and female imputation

Question

[SeoG]

Hello, this is my first time conducting an X chromosome analysis (XWAS).

I have just finished the imputation for female chrX. After QC (filtering out variants with R² < 0.3), 38,312 variants remain.

Does this sound reasonable? I used Minimac3/4 for the imputation and the 1000 Genomes JPT reference panel, since my study cohort is Korean.

Additionally, the original chrX chip data contained only about 900 variants.

Thank you in advance for your advice.

Answer 1

[barslmn]

I think it's better to use the original 900 variants. If you have genotype information, you can get the fraction of heterozygous variants to total variants. The females should be close to 0.5 and males should be close to 0, or 0.1. I have preprint on how to do it here: https://www.biorxiv.org/content/10.1101/2024.12.26.627867v1 Also, if you have VCF files you can use the online tool: https://colab.research.google.com/drive/1ep69JvXLwK5ndHUQ8qIGTWvauzsTW9fi

Since its chip data, software you're using like GenomeStudio should already have option to perform sex estimates. You can also use hail which has a function for sex estimation or plink which has sex estimation too.