gCNV vcf cleanup #6352
gCNV vcf cleanup #6352
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Only called alleles as alts; QS to QUAL
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| @@ -372,7 +374,8 @@ public Object onTraversalSuccess() { | |||
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| private void generateIntervalsVCFFileFromAllShards() { | |||
| logger.info("Generating intervals VCF file..."); | |||
| final VariantContextWriter intervalsVCFWriter = createVCFWriter(outputIntervalsVCFFile); | |||
| final VariantContextWriter intervalsVCFWriter = GATKVariantContextUtils.createVCFWriter( | |||
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Would it be better to use GATKTool's createVCFWriter()?
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The GATKTool method won't accept a sequence dictionary. It relies on the engine discovering a sequence dictionary from one of the inputs, which doesn't work so well here because the inputs are specified as directories.
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Isn’t the dictionary hooked up to createVCFWriter now via getBestAvailableSequenceDictionary?
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Ah yes, this is a holdover from before I implemented that suggestion Louis had. Thanks for the extra set of eyes.
| @@ -412,7 +415,8 @@ private void generateSegmentsVCFFileFromAllShards() { | |||
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| /* write variants */ | |||
| logger.info(String.format("Writing segments VCF file to %s...", outputSegmentsVCFFile.getAbsolutePath())); | |||
| final VariantContextWriter segmentsVCFWriter = createVCFWriter(outputSegmentsVCFFile); | |||
| final VariantContextWriter segmentsVCFWriter = GATKVariantContextUtils.createVCFWriter( | |||
| @@ -128,7 +128,7 @@ VariantContext composeVariantContext(final IntegerCopyNumberSegment segment) { | |||
| int copyNumberCall = segment.getCallIntegerCopyNumberState().getCopyNumber(); | |||
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| final VariantContextBuilder variantContextBuilder = new VariantContextBuilder(); | |||
| variantContextBuilder.alleles(ALL_ALLELES); | |||
| //variantContextBuilder.alleles(ALL_ALLELES); | |||
| @@ -155,8 +155,14 @@ VariantContext composeVariantContext(final IntegerCopyNumberSegment segment) { | |||
| genotypeBuilder.attribute(QSE, FastMath.round(segment.getQualityEnd())); | |||
| final Genotype genotype = genotypeBuilder.make(); | |||
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| final List<Allele> vcAlleles = new ArrayList<>(Collections.singletonList(REF_ALLELE)); | |||
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Could write this as final List<Allele> vcAlleles = Lists.newArrayList(REF_ALLELE);
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Lists is in which package? avro?
Only list called ALTs
Set QUAL to QS (quality of some event), which we've found to be the best for filtering
Resolves most of the rest of #6167