Checking in the liftover script. I am including a post-processing walker to filter out bad records written in under 10 minutes as per my agreement with Mark.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3321 348d0f76-0448-11de-a6fe-93d51630548a
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/*
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* Copyright (c) 2010.
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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
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* 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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*
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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
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* 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
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.walkers.vcf;
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import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
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import org.broadinstitute.sting.utils.BaseUtils;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broad.tribble.vcf.VCFRecord;
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import org.broad.tribble.vcf.VCFCodec;
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import java.util.List;
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/**
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* Filters a lifted-over VCF file for ref bases that have been changed.
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*/
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@Requires(value={},referenceMetaData=@RMD(name="vcf",type= VCFCodec.class))
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public class FilterLiftedVCF extends RodWalker<Integer, Integer> {
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private VCFWriter writer;
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private long failedLocs = 0, totalLocs = 0;
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public void initialize() {}
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private void filterAndWrite(char ref, VCFRecord record) {
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totalLocs++;
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char recordRef = record.getReference().charAt(0);
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if ( recordRef != ref ) {
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// is it reverse complemented?
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if ( BaseUtils.simpleComplement(recordRef) == ref ) {
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record.setFilterString(record.isFiltered() ? String.format("%s;LiftoverToReverseComplementRefBase", record.getFilterString()) : "LiftoverToNewBase");
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failedLocs++;
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} else {
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record.setFilterString(record.isFiltered() ? String.format("%s;LiftoverToDifferentRefBase", record.getFilterString()) : "LiftoverToNewBase");
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failedLocs++;
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}
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}
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if ( writer == null ) {
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writer = new VCFWriter(out);
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writer.writeHeader(record.getHeader());
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}
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writer.addRecord(record);
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}
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( tracker == null )
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return 0;
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List<Object> rods = tracker.getReferenceMetaData("vcf");
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for ( Object rod : rods )
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filterAndWrite(ref.getBase(), (VCFRecord)rod);
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return 0;
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}
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public Integer reduceInit() { return 0; }
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public Integer reduce(Integer value, Integer sum) { return 0; }
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public void onTraversalDone(Integer result) {
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if ( writer != null )
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writer.close();
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System.out.println("Filtered " + failedLocs + " records out of " + totalLocs + " total records.");
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}
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}
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@ -103,7 +103,8 @@ public class LiftoverVCF extends RodWalker<Integer, Integer> {
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public Integer reduce(Integer value, Integer sum) { return 0; }
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public Integer reduce(Integer value, Integer sum) { return 0; }
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public void onTraversalDone(Integer result) {
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public void onTraversalDone(Integer result) {
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writer.close();
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if ( writer != null )
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System.out.println("Converted " + successfulIntervals + " intervals; failed to convert " + failedIntervals + " intervals.");
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writer.close();
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System.out.println("Converted " + successfulIntervals + " records; failed to convert " + failedIntervals + " records.");
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}
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}
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}
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}
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#!/usr/bin/perl -w
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# Runs the liftover tool on a VCF and properly handles the output
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use strict;
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use Getopt::Long;
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my $in = undef;
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my $gatk = undef;
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my $chain = undef;
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my $newRef = undef;
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my $oldRef = undef;
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my $out = undef;
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my $tmp = "/tmp";
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GetOptions( "vcf=s" => \$in,
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"gatk=s" => \$gatk,
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"chain=s" => \$chain,
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"newRef=s" => \$newRef,
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"oldRef=s" => \$oldRef,
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"out=s" => \$out,
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"tmp=s" => \$tmp);
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if ( !$in || !$gatk || !$chain || !$newRef || !$oldRef || !$out ) {
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print "Usage: liftOverVCF.pl\n\t-vcf \t\t<input vcf>\n\t-gatk \t\t<path to gatk trunk>\n\t-chain \t\t<chain file>\n\t-newRef \t<path to new reference prefix; we will need newRef.dict, .fasta, and .fasta.fai>\n\t-oldRef \t<path to old reference prefix; we will need oldRef.fasta>\n\t-out \t\t<output vcf>\n\t-tmp <temp file location; defaults to /tmp>";
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print "Example: ./liftOverVCF.pl\n\t-vcf /humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/1kg_snp_validation/all_validation_batches.b36.vcf\n\t-chain b36ToHg19.broad.over.chain\n\t-out lifted.hg19.vcf\n\t-gatk /humgen/gsa-scr1/ebanks/Sting_dev\n\t-newRef /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19\n\t-oldRef /broad/1KG/reference/human_b36_both\n";
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exit(1);
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}
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# generate a random number
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my $random_number = rand();
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my $tmp_prefix = "$tmp/$random_number";
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print "Writing temporary files to prefix: $tmp_prefix\n";
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my $unsorted_vcf = "$tmp_prefix.unsorted.vcf";
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# lift over the file
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print "Lifting over the vcf...";
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my $cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T LiftoverVCF -R $oldRef.fasta -B vcf,vcf,$in -o $unsorted_vcf -chain $chain -dict $newRef.dict";
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system($cmd);
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# we need to sort the lifted over file now
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print "\nRe-sorting the vcf...\n";
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my $sorted_vcf = "$tmp_prefix.sorted.vcf";
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open(SORTED, ">$sorted_vcf") or die "can't open $sorted_vcf: $!";
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# write the header
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open(UNSORTED, "< $unsorted_vcf") or die "can't open $unsorted_vcf: $!";
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my $inHeader = 1;
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while ( $inHeader == 1 ) {
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my $line = <UNSORTED>;
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if ( $line !~ m/^#/ ) {
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$inHeader = 0;
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} else {
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print SORTED "$line";
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}
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}
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close(UNSORTED);
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$cmd = "grep \"^#\" -v $unsorted_vcf | sort -n +1 | $gatk/perl/sortByRef.pl - $newRef.fasta.fai";
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print SORTED `$cmd`;
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close(SORTED);
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# Filter the VCF for bad records
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print "\nFixing/removing bad records...\n";
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$cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T FilterLiftedVCF -R $newRef.fasta -B vcf,vcf,$sorted_vcf -o $out";
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system($cmd);
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# clean up
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unlink $unsorted_vcf;
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unlink $sorted_vcf;
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print "\nDone!\n";
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