Unified, standard IndelSummary metrics for VariantEval
-- Now you always get SNP and indel metrics with VariantEval! -- Includes Number of SNPs, Number of singleton SNPs, Number of Indels, Number of singleton Indels, Percent of indel sites that are multi-allelic, SNP to indel ratio, Singleton SNP to indel ratio, Indel novelty rate, 1 to 2 bp indel ratio, 1 to 3 bp indel ratio, 2 to 3 bp indel ratio, 1 and 2 to 3 bp indel ratio, Frameshift percent, Insertion to deletion ratio, Insertion to deletion ratio for 1 bp events, Number of indels in protein-coding regions labeled as frameshift, Number of indels in protein-coding regions not labeled as frameshift, Het to hom ratio for SNPs, Het to hom ratio for indels, a Histogram of indel lengths, Number of large (>10 bp) deletions, Number of large (>10 bp) insertions, Ratio of large (>10 bp) insertions to deletions -- Updated VE integration tests as appropriate
This commit is contained in:
Mark DePristo
parent
bcf80cc7b3
commit
6df96644d9
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@ -0,0 +1,230 @@
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/*
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* Copyright (c) 2012, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
|
||||
* files (the "Software"), to deal in the Software without
|
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* restriction, including without limitation the rights to use,
|
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
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* copies of the Software, and to permit persons to whom the
|
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* Software is furnished to do so, subject to the following
|
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* conditions:
|
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*
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* The above copyright notice and this permission notice shall be
|
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* included in all copies or substantial portions of the Software.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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||||
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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||||
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
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import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
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import org.broadinstitute.sting.gatk.walkers.varianteval.util.IndelHistogram;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.variantcontext.Allele;
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import org.broadinstitute.sting.utils.variantcontext.Genotype;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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@Analysis(description = "Evaluation summary for indels")
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public class IndelSummary extends VariantEvaluator implements StandardEval {
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final protected static Logger logger = Logger.getLogger(IndelSummary.class);
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@DataPoint(description = "Number of SNPs", format = "%d")
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public int n_SNPs = 0;
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@DataPoint(description = "Number of singleton SNPs", format = "%d")
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public int n_singleton_SNPs = 0;
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@DataPoint(description = "Number of Indels", format = "%d")
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public int n_indels = 0;
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// Number of Indels Sites (counts one for any number of alleles at site)
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public int nIndelSites = 0;
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@DataPoint(description = "Number of singleton Indels", format = "%d")
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public int n_singleton_indels = 0;
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// counts 1 for each site where the number of alleles > 2
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public int nMultiIndelSites = 0;
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@DataPoint(description = "Percent of indel sites that are multi-allelic")
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public String percent_of_sites_with_more_than_2_alleles;
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@DataPoint(description = "SNP to indel ratio")
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public String SNP_to_indel_ratio;
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@DataPoint(description = "Singleton SNP to indel ratio")
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public String SNP_to_indel_ratio_for_singletons;
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@DataPoint(description = "Indel novelty rate")
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public String indel_novelty_rate;
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@DataPoint(description = "1 to 2 bp indel ratio")
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public String ratio_of_1_to_2_bp_indels;
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@DataPoint(description = "1 to 3 bp indel ratio")
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public String ratio_of_1_to_3_bp_indels;
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@DataPoint(description = "2 to 3 bp indel ratio")
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public String ratio_of_2_to_3_bp_indels;
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@DataPoint(description = "1 and 2 to 3 bp indel ratio")
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public String ratio_of_1_and_2_to_3_bp_indels;
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@DataPoint(description = "Frameshift percent")
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public String frameshift_rate_for_coding_indels;
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//
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// insertions to deletions
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//
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@DataPoint(description = "Insertion to deletion ratio")
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public String insertion_to_deletion_ratio;
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@DataPoint(description = "Insertion to deletion ratio for 1 bp events")
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public String insertion_to_deletion_ratio_for_1bp_indels;
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//
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// Frameshifts
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//
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@DataPoint(description = "Number of indels in protein-coding regions labeled as frameshift")
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public int n_coding_indels_frameshifting = 0;
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@DataPoint(description = "Number of indels in protein-coding regions not labeled as frameshift")
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public int n_coding_indels_in_frame = 0;
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//
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// Het : hom ratios
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//
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@DataPoint(description = "Het to hom ratio for SNPs")
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public String SNP_het_to_hom_ratio;
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@DataPoint(description = "Het to hom ratio for indels")
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public String indel_het_to_hom_ratio;
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int nSNPHets = 0, nSNPHoms = 0, nIndelHets = 0, nIndelHoms = 0;
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int nKnownIndels = 0, nInsertions = 0;
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int n1bpInsertions = 0, n1bpDeletions = 0;
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int[] countByLength = new int[]{0, 0, 0, 0}; // note that the first element isn't used
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public final static int MAX_SIZE_FOR_HISTOGRAM = 10;
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@DataPoint(description = "Histogram of indel lengths")
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IndelHistogram lengthHistogram = new IndelHistogram(MAX_SIZE_FOR_HISTOGRAM, true);
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@DataPoint(description = "Number of large (>10 bp) deletions")
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public int n_large_deletions = 0;
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@DataPoint(description = "Number of large (>10 bp) insertions")
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public int n_large_insertions = 0;
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@DataPoint(description = "Ratio of large (>10 bp) insertions to deletions")
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public String insertion_to_deletion_ratio_for_large_indels;
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@Override public boolean enabled() { return true; }
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@Override public int getComparisonOrder() { return 2; }
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public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( eval == null || eval.isMonomorphicInSamples() )
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return null;
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// update counts
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switch ( eval.getType() ) {
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case SNP:
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n_SNPs += eval.getNAlleles() - 1; // -1 for ref
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if ( variantWasSingleton(eval) ) n_singleton_SNPs++;
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// collect information about het / hom ratio
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for ( final Genotype g : eval.getGenotypes() ) {
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if ( g.isHet() ) nSNPHets++;
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if ( g.isHomVar() ) nSNPHoms++;
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}
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break;
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case INDEL:
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if ( eval.isComplexIndel() ) break; // don't count complex substitutions
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nIndelSites++;
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if ( ! eval.isBiallelic() ) nMultiIndelSites++;
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if ( variantWasSingleton(eval) ) n_singleton_indels++;
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// collect information about het / hom ratio
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for ( final Genotype g : eval.getGenotypes() ) {
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if ( g.isHet() ) nIndelHets++;
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if ( g.isHomVar() ) nIndelHoms++;
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}
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for ( Allele alt : eval.getAlternateAlleles() ) {
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n_indels++; // +1 for each alt allele
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if ( comp != null ) nKnownIndels++; // TODO -- make this test allele specific?
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// ins : del ratios
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final int alleleSize = alt.length() - eval.getReference().length();
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if ( alleleSize == 0 ) throw new ReviewedStingException("Allele size not expected to be zero for indel: alt = " + alt + " ref = " + eval.getReference());
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if ( alleleSize > 0 ) nInsertions++;
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if ( alleleSize == 1 ) n1bpInsertions++;
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if ( alleleSize == -1 ) n1bpDeletions++;
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// update the length histogram
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lengthHistogram.update(eval.getReference(), alt);
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// requires snpEFF annotations
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if ( eval.getAttributeAsString("SNPEFF_GENE_BIOTYPE", "missing").equals("protein_coding") ) {
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final String effect = eval.getAttributeAsString("SNPEFF_EFFECT", "missing");
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if ( effect.equals("missing") )
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throw new ReviewedStingException("Saw SNPEFF_GENE_BIOTYPE but unexpected no SNPEFF_EFFECT at " + eval);
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if ( effect.equals("FRAME_SHIFT") )
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n_coding_indels_frameshifting++;
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else if ( effect.startsWith("CODON") )
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n_coding_indels_in_frame++;
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else
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; // lots of protein coding effects that shouldn't be counted, such as INTRON
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}
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// update the baby histogram
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final int absSize = Math.abs(alleleSize);
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if ( absSize < countByLength.length ) countByLength[absSize]++;
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}
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break;
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default:
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throw new UserException.BadInput("Unexpected variant context type: " + eval);
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}
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return null; // we don't capture any interesting sites
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}
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public void finalizeEvaluation() {
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percent_of_sites_with_more_than_2_alleles = formattedRatio(nMultiIndelSites, nIndelSites);
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SNP_to_indel_ratio = formattedRatio(n_SNPs, n_indels);
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SNP_to_indel_ratio_for_singletons = formattedRatio(n_singleton_SNPs, n_singleton_indels);
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indel_novelty_rate = formattedNoveltyRate(nKnownIndels, n_indels);
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ratio_of_1_to_2_bp_indels = formattedRatio(countByLength[1], countByLength[2]);
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ratio_of_1_to_3_bp_indels = formattedRatio(countByLength[1], countByLength[3]);
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ratio_of_2_to_3_bp_indels = formattedRatio(countByLength[2], countByLength[3]);
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ratio_of_1_and_2_to_3_bp_indels = formattedRatio(countByLength[1] + countByLength[2], countByLength[3]);
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frameshift_rate_for_coding_indels = formattedPercent(n_coding_indels_frameshifting, n_coding_indels_in_frame + n_coding_indels_frameshifting);
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SNP_het_to_hom_ratio = formattedRatio(nSNPHets, nSNPHoms);
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indel_het_to_hom_ratio = formattedRatio(nIndelHets, nIndelHoms);
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n_large_deletions = lengthHistogram.getnTooBigDeletions();
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n_large_insertions = lengthHistogram.getnTooBigInsertions();
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insertion_to_deletion_ratio = formattedRatio(nInsertions, n_indels - nInsertions);
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insertion_to_deletion_ratio_for_1bp_indels = formattedRatio(n1bpInsertions, n1bpDeletions);
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insertion_to_deletion_ratio_for_large_indels = formattedRatio(n_large_insertions, n_large_deletions);
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}
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}
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@ -0,0 +1,113 @@
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/*
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* Copyright (c) 2012, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
|
||||
* files (the "Software"), to deal in the Software without
|
||||
* restriction, including without limitation the rights to use,
|
||||
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
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* copies of the Software, and to permit persons to whom the
|
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* Software is furnished to do so, subject to the following
|
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* conditions:
|
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*
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||||
* The above copyright notice and this permission notice shall be
|
||||
* included in all copies or substantial portions of the Software.
|
||||
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.walkers.varianteval.util;
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import org.broadinstitute.sting.utils.variantcontext.Allele;
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import java.util.*;
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/**
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* Simple utility for histogramming indel lengths
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*
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* Based on code from chartl
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*
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* @author Mark DePristo
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* @since 3/21/12
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*/
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public class IndelHistogram extends TableType {
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private final boolean asFrequencies;
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int nIndels = 0, nTooBigDeletions = 0, nTooBigInsertions = 0;
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private final Integer[] rowKeys;
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private Map<Integer, Double> frequencies = null;
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private final Map<Integer, Integer> counts = new HashMap<Integer, Integer>();
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public IndelHistogram(int maxSize, boolean asFrequencies) {
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this.asFrequencies = asFrequencies;
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initializeCounts(maxSize);
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this.rowKeys = new ArrayList<Integer>(counts.keySet()).toArray(new Integer[maxSize]);
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}
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private void initializeCounts(int size) {
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for ( int i = -size; i <= size; i++ ) {
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if ( i != 0 ) counts.put(i, 0);
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}
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}
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@Override
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public String getRowName() {
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return "Length";
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}
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@Override
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public Object[] getColumnKeys() {
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return new String[]{"Count"};
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}
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@Override
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public Object[] getRowKeys() {
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return rowKeys;
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}
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@Override
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public Object getCell(int row, int col) {
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final int key = (Integer)getRowKeys()[row];
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if ( asFrequencies ) {
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if ( frequencies == null ) {
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frequencies = new HashMap<Integer, Double>();
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for ( final int len : counts.keySet() ) {
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final double value = nIndels == 0 ? 0.0 : counts.get(len) / (1.0 * nIndels);
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frequencies.put(len, value);
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}
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}
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return frequencies.get(key);
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}
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return counts.get(key);
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}
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public int getnTooBigDeletions() {
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return nTooBigDeletions;
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}
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public int getnTooBigInsertions() {
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return nTooBigInsertions;
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}
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public void update(final Allele ref, final Allele alt) {
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final int alleleSize = alt.length() - ref.length();
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update(alleleSize);
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}
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public void update(int len) {
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if ( counts.containsKey(len) ) {
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nIndels++;
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counts.put(len, counts.get(len) + 1);
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} else if ( len < 0 ) {
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nTooBigDeletions++;
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} else {
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nTooBigInsertions++;
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}
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}
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}
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@ -94,7 +94,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-o %s"
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),
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1,
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Arrays.asList("94fb8cba9e236131c6fbf1d7fee738fe")
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Arrays.asList("7a726ecbedd722fa7cd4de3e023b7a82")
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);
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executeTest("testFundamentalsCountVariantsSNPsandIndels", spec);
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}
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@ -115,7 +115,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-o %s"
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),
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1,
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Arrays.asList("670979268b05c3024297ba98d67d89ab")
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Arrays.asList("95bb4a4267a8f29dd7a8169561499f20")
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);
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executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNovelty", spec);
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}
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@ -137,7 +137,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-o %s"
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),
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1,
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Arrays.asList("c38ce9c872a76ae7dd26c3e353bf0765")
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Arrays.asList("9b51029083495935823fb0447a2857b9")
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);
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executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNoveltyAndFilter", spec);
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}
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|
@ -158,7 +158,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-o %s"
|
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),
|
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1,
|
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Arrays.asList("2c37f23bf6114a2b27f21ed445806fd2")
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Arrays.asList("318b5fbbc61e2fc11d49369359812edd")
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);
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executeTest("testFundamentalsCountVariantsSNPsandIndelsWithCpG", spec);
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}
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|
|
@ -179,7 +179,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-o %s"
|
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),
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1,
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Arrays.asList("206f0d629de9af0b97340cb22d34a81b")
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Arrays.asList("74c02df2ef69dda231a2aec2a948747b")
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);
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executeTest("testFundamentalsCountVariantsSNPsandIndelsWithFunctionalClass", spec);
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}
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|
|
@ -200,7 +200,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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"-o %s"
|
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),
|
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1,
|
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Arrays.asList("bd869725429deae8f56175ba9a8ab390")
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Arrays.asList("2d97b1fe15e532e89803ba7ba347ff20")
|
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);
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executeTest("testFundamentalsCountVariantsSNPsandIndelsWithDegeneracy", spec);
|
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}
|
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|
|
@ -221,7 +221,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
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1,
|
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Arrays.asList("9c7f6783a57ad681bb754b5e71de27dc")
|
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Arrays.asList("474cbc231ddbc4ba299ffe61a17405b6")
|
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);
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executeTest("testFundamentalsCountVariantsSNPsandIndelsWithSample", spec);
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}
|
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|
|
@ -244,7 +244,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("a2d280440aa3771937f3d2d10f1eea74")
|
||||
Arrays.asList("2cc9bc4bbe8b4edb6dc27642ec41f66e")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithJexlExpression", spec);
|
||||
}
|
||||
|
|
@ -269,7 +269,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("2925d811dd521beb00059f8c8e818d83")
|
||||
Arrays.asList("00c94cf3e14bc2855d39bbefa27f9bb2")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithMultipleJexlExpressions", spec);
|
||||
}
|
||||
|
|
@ -288,7 +288,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("4b79bf2dfd73ddac0ceb0838a352bf9a")
|
||||
Arrays.asList("a0c0d4805db1245aa30a306aa506096f")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsNoCompRod", spec);
|
||||
}
|
||||
|
|
@ -301,7 +301,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
" --eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
|
||||
" --comp:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
|
||||
WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
|
||||
1, Arrays.asList("1739654de350541edf429888b708ae01"));
|
||||
1, Arrays.asList("2192418a70a8e018a1675d4f425155f3"));
|
||||
executeTestParallel("testSelect1", spec);
|
||||
}
|
||||
|
||||
|
|
@ -329,7 +329,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testCompVsEvalAC() {
|
||||
String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance --eval:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf --comp:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf";
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("d57cf846bc26d338edcf181fb0c85535"));
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("2282523336c24d434d1cc0eb1697b4f9"));
|
||||
executeTestParallel("testCompVsEvalAC",spec);
|
||||
}
|
||||
|
||||
|
|
@ -359,7 +359,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
" --dbsnp " + b37dbSNP132 +
|
||||
" --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
|
||||
" -noST -ST Novelty -o %s";
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("b663745a39f62bfa5b5d486811cf57ec"));
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("ec321fcc424fbad74a4a74e739173d03"));
|
||||
executeTestParallel("testEvalTrackWithoutGenotypes",spec);
|
||||
}
|
||||
|
||||
|
|
@ -371,7 +371,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
" --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
|
||||
" --eval:evalBC " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
|
||||
" -noST -ST Novelty -o %s";
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("f1e1b1469dca86d72ae79a2d3e10612c"));
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("ccaea6245086552cd63f828eabddfaf3"));
|
||||
executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
|
||||
}
|
||||
|
||||
|
|
@ -449,7 +449,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("0c632b5be8a54e43afa576510b40c4da")
|
||||
Arrays.asList("9954c769ef37c47d3b61481ab0807be0")
|
||||
);
|
||||
executeTest("testAlleleCountStrat", spec);
|
||||
}
|
||||
|
|
@ -470,7 +470,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("92404820a94e7cfb854ae73450a0fbd9")
|
||||
Arrays.asList("c0d69ce7647a575d166d8bab5aa16299")
|
||||
);
|
||||
executeTest("testIntervalStrat", spec);
|
||||
}
|
||||
|
|
@ -487,7 +487,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("417875ab1924b7e7950fa10daee393d2")
|
||||
Arrays.asList("9a8ffb506118c1bde6f7bfadc4fb6f10")
|
||||
);
|
||||
executeTest("testModernVCFWithLargeIndels", spec);
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue