Closed nickylustenhouwer closed 9 months ago
Hi, thank you for reaching out!
I think it is me that have a bug somewhere, and will look at it asap. :-)
Best, Jonas
I have now pushed an update that should fix the problem (v1.21)! :-)
Best, Jonas
Hi Jonas,
Thank you so much for taking the time to look into this, I am happy to report that your update has fixed the problem! I now get a sites file of the correct length with 1s and 0s. Many thanks again,
Nicky
I am running pcangsd on a subset of individuals, so when applying the mafs filter, some sites are filtered out. I would like to know which sites were kept, so I can identify them in the final output (for example, label them on a Manhattan plot or compare them between different subsets of the data). I tried doing this using -sites_save:
pcangsd -b call_all_chr1to12_subsampled.beagle.gz --filter samples_Nor.txt -o call_all_chr1to12_subsampled_Nor_pcangsd --threads 5 --iter 300 --pcadapt --snp_weights --admix --admix_iter 300 --sites_save
The output looks normal, and it retained a subset of sites:
Loaded 491259 sites and 334 individuals. Number of sites after MAF filtering (0.05): 383045
I get all of the right output files includingcall_all_chr1to12_subsampled_Nor_pcangsd.sites
Everything else works (covariance matrix, zscores, SNP weights) but the sites file contains only 0s! It has the correct number of lines - 491259 - but every single line has a 0, so there is no way for me to know which sites were kept and which sites weren't. All of the other output files contain the filtered number of sites (383045).What could I be doing wrong? I tried running pcangsd without -filter, or without -admix or -pcadapt but no matter what I do -sites_save only returns zeros. Many thanks for your help!