These are chat archives for dereneaton/ipyrad

Apr 2017
Mariska Brady
Apr 16 2017 03:10 UTC
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Mariska Brady
Apr 16 2017 03:16 UTC
I'm analyzing a ddRAD dataset using only read 1 and I’m experiencing some interesting output in my *.u.snps.phy files. In particular, the output is producing numerous loci that aren't actually variable across my dataset. Instead, they contain a single nucleotide and N, only. For this particular file, only 1,710 loci out of the original 4,304 in the file are truly variable (def: 1 or more individual actually has a different nucleotide or is heterozygous at the locus). FYI, I've stipulated 12X coverage with 40% of individuals sharing the locus. An image of the alignment with some representative loci is attached. I’m curious if you know what’s happening here? Am I missing something?
Isaac Overcast
Apr 16 2017 11:52 UTC
@Maricatekins_twitter Can you email me the *.u.snps.phy file? I can't really tell what's happening w/o seeing the whole file. I'll pm you my email address. Read depth and sample coverage shouldn't change the fact that the .snps.phy file should only include variable sites.