I am mapping to mouse genome using HISAT2 and graph index (created using SNPs and InDels). The problem is that although HISAT2 finds alignments over the SNPs in the graph, it finds no alignments over InDels.
I am using one chromsome, where I have around 288K SNPs and 36K InDels in the Index (counted using hisat2-inspect). I know there are reads in my test data that align over InDels. I tried using version 2.0.4 and 2.0.5.
I posted this issue on GitHub and also on the HISAT2 mailing list, but haven't heard from the authors so far. Does anyone come across this issue and can it be solved by changing one of the mapping parameters?