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Using James P's patch for the liftover script 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4515 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2010-10-18 01:44:54 +00:00
parent 6af9532090
commit f962039273
1 changed files with 3 additions and 3 deletions
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6
perl/liftOverVCF.pl
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@ -54,11 +54,11 @@ while ( $inHeader == 1 ) {
}
}
close(UNSORTED);
$cmd = "grep \"^#\" -v $unsorted_vcf | sort -n -k2 -T $tmp | $gatk/perl/sortByRef.pl --tmp $tmp - $newRef.fasta.fai";
print SORTED `$cmd`;
close(SORTED);
$cmd = "grep \"^#\" -v $unsorted_vcf | sort -n -k2 -T $tmp | $gatk/perl/sortByRef.pl --tmp $tmp - $newRef.fasta.fai >> $sorted_vcf";
system($cmd);
# Filter the VCF for bad records
print "\nFixing/removing bad records...\n";
$cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T FilterLiftedVariants -R $newRef.fasta -B:variant,vcf $sorted_vcf -o $out";