These are chat archives for dereneaton/ipyrad

12th
Dec 2018
jhoepke
@jhoepke
Dec 12 2018 13:58
Hello, I would like to know if it is possible to make a tetraploid snp call in ipyrad since I have GBS data including diploids and tetraploids? My goal would be to get a GT:DP:CATG-output in the vcf-file that looks like this "0/0/0/1:15:15,0,0,0" and str-files with four rows per individual. I was already thinking about to use GATK to make a tetraploid snp call but my denovo runs in ipyrad do not store any kind of bam-files whereas my reference runs do?! Many thanks in advance!