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Rosemeis / pcangsd

Framework for analyzing low depth NGS data in heterogeneous populations using PCA.
GNU General Public License v3.0
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How to format a --filterSites file? #66

Open TeresaPegan opened 1 year ago

TeresaPegan commented 1 year ago

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 commented 1 year ago

Hi Teresa,

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

Best, Jonas