I'm using the latest version of Pindel (0.2.5b9, 20160729) for somatic DNA to detect internal tandem duplications (ITDs) at variant allele frequencies (VAFs) in the range of 5% and greater. The vcf files produced by pindel2vcf always report 0 as the allele depth (AD) for the reference allele. Supposedly Pindel's VCFs also have a "reference depth" metric (RD) but this is not actually reported.
I cannot find anything in the raw Pindel output (such as the _TD file) that corresponds to an allele frequency or reference depth.
One (ugly) idea I have is to get total depth from something like GATK's DepthOfCoverage and divide that by Pindel's alt allele depth?
Is there a more elegant/correct solution to this issue?