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Why is HaplotypeCaller not calling obvious SNPs by default but requires -allowNonUniqueKmersInRef?
I'm calling SNPs for bacterial genomes. I've been using UnifiedGenotyper to call SNPs, and I'm looking to migrate to HaplotypeCaller. This change from UnifiedGenotyper to HaplotypeCaller requires validating SNPs being called. I've came across a situation where a SNP is being called in only some genomes using the HaplotypeCaller, but the SNP is clearer present in all genomes when visually validated in IGV. After trying many HaplotypeCaller arguments, only when using -allowNonUniqueKmersInRef was the position correctly called in all genomes. Can you describe what this flag is doing to allow the position to be called correctly in all genomes, and describe why when using the default HaplotypeCaller parameters this SNP is not found in all?
This is the position when called using -allowNonUniqueKmersInRef.
gi|561108321|ref|NC_018143.2| 3336835 . T C 1278.77 . AC=2;AF=1.00;AN=2;DP=44;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.18;MQ0=0;QD=29.06;SOR=0.739 GT:AD:DP:GQ:PL 1/1:0,43:43:99:1307,128,0