Accurate ref/alt read counts for DNPs
I am using HaplotypeCaller in "genotype_given_alleles" mode in order to obtain REF and ALT read counts for candidate variants (using the AD field). This seems to work fine for SNPs and indels; however, I seem to have trouble with DNPs (e.g. REF=CC,ALT=AT), which always get assigned a variant read count of zero (e.g. "GT:AD:DP:GQ:PL 0/0:331,0:331:99:0,1072,2147483647". When I look at the HC-generated bam in a viewer, the variant reads are clearly present in abundance. So the read stats seem to be wrong.
Is this expected behavior? If not, could you recommends steps/checks to figure this out?
I have attached my HC parameters, a list of some DNPs that were missed, and a screen shot of the first variant.