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