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VariantAnnotator issue with trios!
First I have to express my appreciation for great tools and the support we are getting from The Broad Institute on this forum.
Following BestPractices, I ran the VariantAnnotator walker on GATK 3.8 with the "PossibleDeNovo" annotation option together with .ped file for the families in the re-calibrated vcf. However, I ran across the following two interesting results:
- One hiConfDeNovo variant was called for the proband, with a 0 value for the AD (Allelic Depths), and only 2 for the proband. Upon examining the bam files for both, the father had actually four reads in that area with the alternative variant, yet all four of them had low mapping quality; therefore it was changed from 1/1 before recalibration to 0/0 with 0 AD after calibration.
- A variant was discovered previously via WES using different tools, but I couldn't find it as de novo in the call set. Upon going back to the recalibrated vcf, I found that the variant was present int he proband, and absent for both parents, with good coverage for the three of them. It has not been called as a de novo with VariantAnnotator, not even as a loConfDeNovo.
I believe that the recalibration process was done nicely, but the VariantAnnotator is behaving in a very weird way.
This is the command line I used:
$ java -jar /path/to/GenomeAnalysisTK.jar -T VariantAnnotator -R /path/to/ref.fasta -V recalibratedVariants.postCGP.Gfiltered.vcf -A PossibleDeNovo -ped trios.ped -o recalibratedVariants.postCGP.Gfiltered.deNovos.vcf