DepthOfCoverage only analyzing one gene of two overlapping genes

I ran DepthOfCoverage on several samples for ~5000 genes. It turns out that a handful (~30) of these genes are overlapping (but on different strands). In these cases, it seems that DoC analyzes the first overlapping gene but not the second overlapping gene. For example, in this case (below), it will produce depth stats for the first interval, but not the second interval. You can see the end of the first interval 495620 is actually bigger than the beginning of the second interval 494949.

Pv_Sal1_chr14:493199-495620  ## On (-) strand
Pv_Sal1_chr14:494949-495542  ## On (+) strand

Is there a way to force DoC to analyze overlapping intervals? I'm using GATK v3.2.2 with the following command:

java -jar GenomeAnalysisTK.jar -T DepthOfCoverage -R ref.fasta -I bamnames.list -o coverage/test.cov -geneList coverage/test.refseq -L coverage/test.intervals -omitBaseOutput --minMappingQuality 20 --minBaseQuality 20

Thanks for any help!

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  • cparobekcparobek Member

    @Geraldine_VdAuwera‌ - Thanks for your answer. I'll try DiagnoseTargets as well as separating by strand - the separate-by-strand solution is more elegant than the solution I was contemplating.
    Thanks!

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