How to format a --filterSites file?

[TeresaPegan]

Hi! I would like to use the --filterSites argument with PCANGSD but I can't find anywhere that describes how to formate the file passed to this argument.

Based on the code and a little bit of troubleshooting, I think it looks like it's supposed to be similar to the ind sites file where sites are included or excluded on the basis of a file of 0s and 1s. So, if I have a beagle file with 10 SNPs in it and I only want to use the latter half, is this what the --filterSites file should look like?

0
0
0
0
0
1
1
1
1
1

Thanks,
-Teresa

[Rosemeis]

Hi Teresa,

Yes, you are right! And sorry for the documentation not being up to date.

Best,
Jonas