I am trying to use DiscoSNP++ v2.3 on a data set of 30 individuals (Illumina resequencing, 100/150 bp reads and 25 to 50x coverage depending on the individual).
I get a lot of missing data (./.), probably because for a lot of detected SNP, a high proportion of individuals do not have enough reads mapped by the kissreads module. I suspect part of the problem is I am working with a very heterozygous species, with a high SNP density in some genomic regions.
I tried different values for the max number of polymorphism (-P) and the number of authorized substitutions while mapping reads (-d), with no real improvement. Does someone have a suggestion to try to fine tune parameters for my case?
Thank you in advance for your answer. Yann