Test-drive the GATK tools and Best Practices pipelines on Terra
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SNP calling for Haploid Genomes
I used both haploid version (-ploidy flag set to 1) and the default version of UG to call SNPs between a reference assembly and sequence reads that come from the same haploid genome.
In the former case I get about 125 alt. hom calls and in the diploid mode of calling about 1,140 het and 120 alt. hom SNPs. Since the comparison is being done within haplotypes, I don’t expect any variation at all. What could be the basis for noise that is observed?
Thank you for your input!