Question: Obtaining list of / manually specifying interrogation sites in Peddy
2
gravatar for gaelgarcia
2.4 years ago by
gaelgarcia190
UK
gaelgarcia190 wrote:

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.

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by gaelgarcia190
2
gravatar for brentp
2.4 years ago by
brentp23k
Salt Lake City, UT
brentp23k wrote:

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

ADD COMMENTlink written 2.4 years ago by brentp23k

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?

ADD REPLYlink written 2.4 years ago by gaelgarcia190
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