I'm trying to figure out what the list of SNPs interrogated by [Peddy][1] is, and how one can manually specify the sites to look at, as stated in [their paper][2]:

> 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.


  [1]: https://github.com/brentp/peddy/blob/master/README.md
  [2]: https://www.sciencedirect.com/science/article/pii/S0002929717300174?via%3Dihub
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