GenotypeGVCFs produces bizarre mapping quality distribution
Hello everybody!
Why would I only see mapping qualities less than or equal to 40 for all called variants? GenotypeGVCFs for 37 non-model organism individuals produces the same distribution of mapping qualities for all chromosomes where there is a continuous range of mapping qualities starting at MQ=20 until MQ=40 where it abruptly stops. However, there is an unusually high frequency of calls with exactly MQ=40.
This is my first try at SNP calling, and I am at a loss for an explanation for this pattern. The attached image is a histogram of MQ for all unfiltered called variants for one chromosome. The pattern is the exact same for all chromosomes.
Thanks!!!
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Hi Daniel Nondorf,
Thank you for writing in. This may be an expected result just depending on your input data and what tools you have run. Can you take a look at the default read filters listed in the HaplotypeCaller documentation that are automatically applied to see if this helps explain your results? (or similar documentation for tools you ran prior to GenotypeGVCFs) If this is not helpful, could you provide more information about your data and the tools you have run so far?
Kind regards,
Pamela
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