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.
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
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?
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