Docs for M2 filtering #3560
Docs for M2 filtering #3560
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| \item \code{maxEventsInHaplotype} is the maximum allowable number of called variants co-occurring in a single assembly region. If the number of called variants exceeds this they will all be filtered. Note that this filter is misnamed because it counts the total number of events over all haplotypes in an assembly region. | ||
| \item \code{uniqueAltReadCount} is the minimum number of unique (start position, fragment length) pairs required to make a call. This count is a proxy for the number of unique molecules (as opposed to PCR duplicates) supporting an allele. Normally PCR duplicates are marked and filtered by the GATK engine, but in UMI-aware calling this may not be the case, hence the need for this filter. | ||
| \item \code{maxAltAllelesThreshold} is the maximum allowable number of alt alleles at a site. By default only biallelic variants pass the filter. | ||
| \item \code{max\_germline\_posterior} is the maximum posterior probability, as determined by the above germline probability model, that a variant is a germline event. |
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I think we should just use to lowerCamelCase and not names_with_underscores. Could you also standardize them in M2FiltersArgumentCollection, too? For instance STRAND_ARTIFACT_POSTERIOR_PROB_THRESHOLD should be strandArtifactPosteriorProbThreshold and TUMOR_LOD_THRESHOLD tumorLodThreshold.
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I agree, but there's discussion about standardizing all GATK argument to eg strand-artifact-posterior-prob-threshold and I'm waiting to see about that. Personally I think camel case is superior. If HaplotypeCaller doesn't adopt a standard within a few weeks, then let's do camel case.
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| \begin{itemize} | ||
| \item \code{tumor\_lod} is the minimum likelihood of an allele as determined by the somatic likelihoods model required to pass. | ||
| \item \code{maxEventsInHaplotype} is the maximum allowable number of called variants co-occurring in a single assembly region. If the number of called variants exceeds this they will all be filtered. Note that this filter is misnamed because it counts the total number of events over all haplotypes in an assembly region. |
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should we rename the variable then?
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Yeah, I think I'll do it after the comms team's upcoming tutorial.
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| Here for convenience is a table of \code{Mutect2} filters with their corresponding annotations specified by the \code{-A} argument\footnote{Most of these are default annotations and do not need to be invoked explicitly.}, vcf keys for these annotations, and command line arguments controlling filtering thresholds. | ||
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| \begin{table}[h!] |
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Once we update the variable names we should update the argument column
davidbenjamin
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## master #3560 +/- ##
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Coverage 79.932% 79.932%
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@takutosato can you review this?