Chromosome X

[Daniel E. Weeks]

Most analysis programs are developed first for autosomal data, and then later generalized/adjusted to work on X data.

We are applying Genotype Harmonizer to X chromosomal data in the pseudo-autosomal regions (PAR) and non-PAR region, and were wondering if Genotype Harmonizer's algorithms handle chromosome X data properly? There doesn't seem to be a switch to inform it that it is analyzing X chromosome data instead of autosomal data.

Thank you,
Dan Weeks

[Patrick Deelen]

Dear Dan,

In principle Genotype Harmonizer will handle chr X files correctly. However, the LD based strand alignment is not available for chr X.

Patrick