haplotypecalling of side-by-side variants homo/hetero

Hi,

we currently observed several cases were we find hetero/homo variants in to continous positions. Looking on the BAM file verifies that the variants are on the same allele/reads.
The GATK HaplotypeCaller will always call these variants as two single variants whereas for example freebayes will call it as a single variant.

e.g. in VCF file format:

GATK
10 123123123 G A ...
10 123123124 C A ...

freebayes
10 123123123 GC AA ...

Why is GATK Haplotypecaller not combining these two variants, since we are interested in the haplotype? Did I miss a flag for the command line etc. ?

Best.

Marten

Issue · Github
by Geraldine_VdAuwera

Issue Number
891
State
closed
Last Updated
Closed By
vdauwera

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