custom sites

[cartographerJ]

Not really an issue, just looking for guidance ( I don't really understand the .bin file for the sites) on how to take a 1000 genomes vcf filtered to specific SNPs present commonly in our data and create the bin file for [eddy to do ancestry. I know that this is depreciated in favor of somalier but it seems like the ancestry imputation in peddy is more stable.

[brentp]

With peddy, you must simply use the sites you have and hope they overlap sufficiently with the sites that peddy uses.

Indeed, somalier would be a good replacement, but I need to allocate some time to work on the ancestry stuff.

[cartographerJ]

So it's not possible to just make custom versions of these files?

GRCH38.sites
GRCH38.sites.bin.gz

[brentp]

I suppose you could do that and just replace them in the peddy install.