Holiday Notice:
The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!

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?


Sign In or Register to comment.