Tool:A notebook for checking relatedness and X heterozygosity from sequencing data

Question

[barslmn]

Tool can be accessed here.

Result of the demo study can be accessed here.

Source can be accessed here.

While working with sequencing data we require check for relatedness and samples' sexes. This can be useful for identifying mix-ups and seeing which sample are related or validating repeat samples. In background, it uses vcftools relatedness2 package. This does not perform a Mendelian check so it doesn't validate the parents.

[Jeremy Leipzig]

What would this return for individuals with Klinefelter syndrome i.e. XXY?

[barslmn]

I haven't got the chance to work with any sex chromosome number anomalies with sequencing data. For XXY, since Y brings in gametolog genes/regions that show homology with X I would except it to be a bit higher than XX. But can't be sure if it is the case, or it can be detectable without testing with data. Any other X and Y combinations would also be interesting.