The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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.