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HaplotypeCaller does not call all variants
I am implementing my pipeline to Roche and I have a list of variants that are validated with Sanger.
In my pipeline I am using HaplotypeCaller to call variants, but there are variants that are not called. I have seen the bam file with IGV and I have found those variants in my reads.
- I have SNP at this coordinate of BRCA2: 32906729 (A->C), the reads with this snp are 100% (150 reads in total)
- I have SNP at this coordinate of BRCA1: 41215825 (G->A), the reads with this snp are 100% (260 reads in total)
but I have not found they in my vcf.
Why is there this problem? Could you help me? Thank you in advance