Question: How to get variant allele frequency (VAF) for internal tandem duplications (ITDs) from Pindel?
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9 weeks ago by
myourshaw0 wrote:

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?

pindel • 83 views
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