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HC missing SNPs
HC does not detect a small number of SNPs that appear very clearly in the alignment. HC reported >4k variants, some with much more challenging alignments, so I just can't figure out why it misses some of these variants since the conditions look ideal for detection. In the sample NA12878, the C/T variant at chr15:66735551 has the following characteristics:
1. The ratio of C:T alleles is 55:45, and A,G and N are all 0%.
2. Base qualites are high for both alleles: upper 20s to lower 30s.
3. Mapping qualities are high: ~70.
4. There are no nearby indels or unusual variants/sequencing errors.
Looking at the reassembled bam, the SNP is present almost completely unchanged, as seen in the lower panel in the screenshot.
I am using v3.3 with default settings and I also tried --maxNumHaplotypesInPopulation 500 --kmerSize 25