I am running the TASSLE4-GBS pipeline in Barley with a reference genome that was created by taking the Morex contigs and concatenating them together, separated by a series of 64 N's. When I look at the hapmap output files, I find a very small percentage of loci that have SNP variant calls for which the Reference allele is reported to be "A", yet the reference allele is an "N".
I have looked in-depth at two chromosomes so far and for the first, I have 6969 reported SNPs, 12 of which are "N" in the reference, and yet the hapmap file states they are "A" and calls SNPs. For the second chromosome, I have 11787 reported SNPs, 20 of which have this error. In these errors, the reference allele is always reported as "A". I have confirmed that the bases at the reported positions are "N" using 'cut' in Unix.
Many of these "N" sites that have SNPs being called are in the 64bp "N" linker regions, but some are also being called at "N" positions within a contig.
I can provide files, if needed. I'm just wondering if anyone else has experienced these issues?
