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Missing variant while useing HaplotypeCaller
We are analysing monozygotic twins while using the HaplotypeCaller but we see some weird things. Not all SNPs are seen by the HaplotypeCaller while the bam file as input has clearly the SNP in there, this while in the twin it is called.
I did let the HaplotypeCaller output a bamfile and it seems that the haplotypecaller does not seem to use any reads on this SNP. In the igv screenshot there are the gvcf files of both samples and the pre-haplotypecaller bam and the post-haplotypecaller bam.
The pre-bams have used the indelrealignment and baserecalibration like in the best practice.
There multiple of this locations so this screenshot is just an example.
Someone know why this is caused and maybe how to solve this?