72 lines
2.5 KiB
Perl
Executable File
72 lines
2.5 KiB
Perl
Executable File
#!/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 \t\t<temp file location; defaults to /tmp>\n";
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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 LiftoverVariants -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 -k2 -T $tmp | $gatk/perl/sortByRef.pl --tmp $tmp - $newRef.fasta.fai";
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print SORTED `$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 FilterLiftedVariants -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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