When using the GATK pipeline to call variants, I end up obtaining a DP for each variant skewed towards 50 and multiples of 50 (see photo below) when my average read depth from my sequencing files should be much less than 50. What could be causing this bias and how might I fix it?
If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: gatk-188.8.131.52
b) Exact command used: I am not sure which command in my script is causing the bias.
c) Entire error log: N/A
If not an error, choose a category for your question(REQUIRED):
a)How do I (......)?
b) What does (......) mean?
c) Why do I see (......)?
d) Where do I find (......)?
e) Will (......) be in future releases?
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