Calculate and Store site-level QCs #7197
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| CreateFilteringFiles \ | ||
| --ref-version 38 \ | ||
| --filter-set-name ~{filter_set_name} \ | ||
| -mode SNP \ | ||
| -V ~{snp_recal_file} \ | ||
| -O ~{filter_set_name}.snps.recal.tsv | ||
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| gatk --java-options "-Xmx4g" \ | ||
| gatk --java-options "-Xmx1g" \ |
| omitFromCommandLine = true | ||
| ) | ||
| public final class CreateSiteFilteringFiles extends VariantWalker { | ||
| static final Logger logger = LogManager.getLogger(CreateVariantIngestFiles.class); |
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should this use CreateSiteFilteringFiles.class instead?
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| private SimpleXSVWriter writer; | ||
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| private List<String> HEADER = |
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for consistency with other tools, move this to SchemaUtils ?
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my future self thanks you
mmorgantaylor
approved these changes
Apr 12, 2021
| @@ -234,6 +252,14 @@ private void processVQSRRecordForPosition(ExtractFeaturesRecord rec) { | |||
| } | |||
| builder.attribute(GATKVCFConstants.EXCESS_HET_KEY, String.format("%.3f", excessHetApprox)); | |||
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| if (rec.getDistinctAlleles() > 6) { | |||
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is this a constant defined somewhere that we can use? (or should we make it one?)
| @@ -75,6 +75,9 @@ public static VCFFormatHeaderLine getEquivalentFormatHeaderLine(final String inf | |||
| addFilterLine(new VCFFilterHeaderLine(VCFConstants.PASSES_FILTERS_v4, "Site contains at least one allele that passes filters")); | |||
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| addFilterLine(new VCFFilterHeaderLine(NAY_FROM_YNG, "Considered a NAY in the Yay, Nay, Grey table")); | |||
| addFilterLine(new VCFFilterHeaderLine(EXCESS_ALLELES, "Site has an excess of alternate alleles")); | |||
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if the excess alleles number (6) was a constant somewhere, you could put that into the header. (maybe users don't care, but i would personally find it helpful!)
src/main/java/org/broadinstitute/hellbender/tools/variantdb/nextgen/ExtractFeaturesRecord.java
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This was referenced Mar 17, 2023
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Addresses 219
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feature_extract.sqllocationfieldsMinor changes