What do the two different minimum base quality filters do in Mutect2?
There are 2 base quality filters in mutect2. What is the difference between them?
1:
| --f1r2-min-bq | 20 |
exclude bases below this quality from pileup |
2:
|
--min-base-quality-score -mbq |
10 | Minimum base quality required to consider a base for calling |
What is the difference between these?
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Hi Nick Bernstein,
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I haven't found any information about f1r2-min-bq, but here is GATK issue that goes into the min-base-quality-score parameter a bit (https://github.com/broadinstitute/gatk/issues/6045)
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Hi Nick Bernstein, Alijah O'Connor,
We addressed this question in our round up of Mutect2 forum questions in the FAQ. You can find the answer and other answers in this doc: https://gatk.broadinstitute.org/hc/en-us/articles/360050722212-FAQ-for-Mutect2
Genevieve
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