These are chat archives for dereneaton/ipyrad

31st
Jan 2019
jhoepke
@jhoepke
Jan 31 15:34
@isaacovercast I wanted to determine allelic ratios for identifying paralogs (according to McKinney et al. 2017, Mol. Ecol. Resources) but ipyrad version 0.7.28 generates a lot of ill-formatted heterozygous genotypes (below you can see one example SNP row from the .vcf file). These genotypes have only depth counts for one allele (e.g. 0/1:32:32,0,0,0). What is with the other allele? How can I access this missing information or are those genotypes simply incorrect called from ipyrad and should be homozygous instead?
locus_426    147    .    G    T    13    PASS    NS=7;DP=212    GT:DP:CATG    ./.:0:0,0,0,0    0/0:20:0,0,2,18    ./.:0:0,0,0,0    ./.:0:0,0,0,0    ./.:0:0,0,0,0    0/0:7:0,0,0,7    0/0:21:0,0,21,0    0/0:103:102,1,0,0    ./.:0:0,0,0,0    ./.:0:0,0,0,0    ./.:0:0,0,0,0    0/1:9:9,0,0,0    0/1:32:32,0,0,0    0/0:20:0,0,2,18
And this problem does NOT only occur for some single genotypes ... unfortunately.