These are chat archives for dereneaton/ipyrad

11th
Aug 2017
Bohao Fang
@fangbohao_twitter
Aug 11 2017 10:08
Hi @dereneaton, the problem of BUCKy "import ipyrad.analysis as ipa" is still over there. Should I undate something?
markb729
@markb729
Aug 11 2017 13:48
Hi @dereneaton - I found an issue regarding iPyrad's adherence to VCF specifications. Not sure what is causing it, but it is an allele mismatch, specifically the allele ID is [sometimes] larger than the number of alleles. For example, locus_92 111 . A T,C 13 PASS NS=20;DP=118 GT:DP:CATG ./.:0:0,0,0,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0./.:0:0,0,0,0 ./.:0:0,0,0,0 1/0:14:1,8,5,0 3/3:1:0,0,0,1 1/0:7:0,3,3,1 ./.:0:0,0,0,0 ./.:6:0,2,4,0 0/0:1:0,1,0,0 2/2:1:1,0,0,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 1/0:9:0,8,0,1 ./.:0:0,0,0,0 1/1:1:0,0,1,0 ./.:0:0,0,0,0./.:0:0,0,0,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 ./.:4:0,2,2,0 ./.:0:0,0,0,0 1/0:5:3,0,0,2 ./.:4:1,0,0,3 0/0:1:1,0,0,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 ./.:1:1,0,0,0 1/0:3:3,0,0,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0 ./.:0:0,0,0,0./.:0:0,0,0,0 ./.:0:0,0,0,0 1/0:11:0,11,0,0 1/0:12:0,5,7,0 ./.:6:0,5,1,0 ./.:0:0,0,0,0 1/0:7:0,1,6,0 1/0:22:2,10,10,0 ./.:2:2,0,0,0
Note the presence of 3/3:1:0,0,0,1 in this pasted sample string. This is definitely not possible. Could you take a look into this?
Deren Eaton
@dereneaton
Aug 11 2017 16:02
Hi @markb729, I see the problem, thanks for pointing it out. It looks like we are only listing up to two alternative alleles, even though there could be three. When I check in the .loci file at the locus and site where a 3/3 occurs in one of my data sets I see that there is in fact a third base there. So the base call is correct, just not the listing of observed bases (i.e., T,C should be T,C,G). Working on a fix.