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2. Documentation Questions
3. What do the two different minimum base quality filters do in Mutect2?

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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• Alijah O'Connor
• December 18, 2020 15:35
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3. Interval Filtering -- How does it actually work?

Thank you!  Yes, this very helpful in understanding exactly what behavior to expect when I'm using this parameter.

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• Alijah O'Connor
• September 21, 2020 22:53
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2. Other
3. Interval Filtering -- How does it actually work?

For sure, but I'm more trying to get at the exact operations that are going on under the hood.  The documentation doesn't really help with the questions I posed in the original post. An additional ...

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• Alijah O'Connor
• September 18, 2020 21:45
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2. Somatic
3. CrosscheckFingerprints EXIT_CODE_WHEN_MISMATCH doesn't seem to work

This appears to be a python problem: Tool returned (STDOUT): -42 (which is the value I set for EXIT_CODE_WHEN_MISMATCH) Python exit code (via subprocess.call()): 4

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• Alijah O'Connor
• July 22, 2020 18:16
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3. Interpretting CrosscheckFingerprints metrics

Thanks for clarifying some of this Bhanu Gandham, though I would like to mention that compared to many of the other GATK tools, I find the documentation of this tool to be quite confusing. I'm not ...

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• Alijah O'Connor
• July 09, 2020 22:51
• 1 vote

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2. Somatic
3. Interpretting CrosscheckFingerprints metrics

There are no descriptions for the fields at http://broadinstitute.github.io/picard/picard-metric-definitions.html#CrosscheckMetric either

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• Alijah O'Connor
• March 12, 2020 22:12
• 0 votes