haplotypecalling of side-by-side variants homo/hetero
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:
10 123123123 G A ...
10 123123124 C A ...
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. ?