Brent Pedersen

ancestry uses PCA. a sample without hom-ref calls will cluster away from all other samples which have hom-ref, het and hom-alt, so this will not be useful. I am trying...

that means your VCF has samples that are not in the ped file. can you post the full output? and the output of `zgrep -m1 CHROM $vcf` ?

This is odd. There must be somethign odd about your ped file. Can you post it here or email it to me? what is the output of cut -f 1...

ok. the ped file for peddy only needs the first 6 columns. Seems like you might have an empty row (maybe at the end?)

you should use tabs. and make sure you don't have any empty lines at the end of the file. is it possible that you have a really old version of...

can you install the cyvcf2 from bioconda? otherwise, you'll need libcrypto and libcurl and likely liblzma

It might be because of this: https://github.com/brentp/peddy/blob/master/peddy/peddy.py#L133 Instead of working on peddy, you might try [somalier](https://github.com/brentp/somalier) it's faster and scales to more samples.

187 thousand samples!? That is too big for peddy. You might try [somalier](https://github.com/brentp/somalier) on batches of ~20 thousand at a time.

do you mean for peddy? no. i would just use somalier for 20K at a time. in order to compare all pairwise combinations for your samples, you'd need to do:...

can you share the ped file?