Obtaining list of / manually specifying interrogation sites in Peddy

Question

[gaelgarcia]

I'm trying to figure out what the list of SNPs interrogated by Peddy is, and how one can manually specify the sites to look at, as stated in their paper:

Given a VCF file and associated PED file describing the expected relationships and sex of the individuals in a sequencing study, peddy automatically conducts all of the tests described using the subset of 23,556 informative SNPs, thereby allowing the rapid detection of possible issues with individual samples. [...]

We emphasize that the user may also specify their own selection of sites [...]

Does anyone have any experience with this?

Thank you.

Answer 1

[brentp]

Here is the current list of sites: https://github.com/brentp/peddy/blob/master/peddy/1kg.sites

There is a grad student in the lab working on allowing any set of sites (so we can support hg38 and any genome build). I hope this will be out soon, but I think he has some work yet to do. You can track the progress here: https://github.com/brentp/peddy/issues/33

[gaelgarcia]

Thanks, Brent. We're currently trying to do identity checks on targeted sequencing data from ~15K samples. However, our panel is very specific, and only a very small fraction of the sites interrogated by Peddy are covered. Is there a similar tool you can recommend for our specific case?