SNP calling for the X chromosome

[TimHasenbein]

trafficstars

Hi,

Thank you for developing this great tool! I have a question regarding calling X chromosomal SNPs in female samples. Given that X chromosome inactivation occurs randomly, single-cell data should contain reads from both X chromosomes across the cell population.

Is it possible to call germline variants for the X chromosome in this context?

I appreciate your help and look forward to your insights.

Best regards, Tim