Why do I see the Artificial Haplotype RG add more heterozygosity?
In the top part we have the bam file after using HaplotypeCaller with the option --bamfile. In the lower part there is the bam file after mapping with BWA-MEM.
We can see that the Artificial HaplotypeCaller adds 120 reads to T, and thus when variants are called this position gets called as an heterozygote.
How can it be that 2 T's can have such a large influence that it adds 120 more?
Thanks in advance.
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