Obtaining list of / manually specifying interrogation sites in Peddy
Entering edit mode
3.1 years ago
gaelgarcia ▴ 190

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.

SNP peddy pedigree identitycheck • 829 views
Entering edit mode
3.1 years ago
brentp 23k

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

Entering edit mode

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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