I've called WGS Drosophila variants using GATK UnifiedGenotyper.
My problem is that the distribution of the quality scores is very asymmetrical, effectively with one very high peak of comparatively low quality and one secondary peak of greater quality.
I don't strictly know if this a cause for concern but it really doesn't look right to me.
My read mapping pipeline includes removal of adaptors and low-quality bases, and local re-alignment. The variant call quality scores are from four individuals with an average of 30X coverage.
Any advice on whether I should be concerned and what I might be able to do to correct this would be much appreiciated.
My problem is that the distribution of the quality scores is very asymmetrical, effectively with one very high peak of comparatively low quality and one secondary peak of greater quality.
I don't strictly know if this a cause for concern but it really doesn't look right to me.
My read mapping pipeline includes removal of adaptors and low-quality bases, and local re-alignment. The variant call quality scores are from four individuals with an average of 30X coverage.
Any advice on whether I should be concerned and what I might be able to do to correct this would be much appreiciated.
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