We are trying to find SNPs in a few loci of interest in rhesus macaque. To that end, we have sequenced exome sequences and I've gone through the process of calling SNPs using GATK and I've come up with a multi-sample VCF file.
Now we want to actually create alternative fasta references for each macaque at our loci of interest. I thought that Novocraft utility "novoutil iupac" would do exactly what I want it to do.
However, I'm receiving the following error:
"Loading VCF file...
novoutil: src/vcfsnps.cc:152: bool vcffile::hetero(tabbed&): Assertion `*gt == '|' || *gt == '/'' failed."