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Stupid cent_os doesn't allow old style 'sort' conventions. Updating liftover script... 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3577 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2010-06-17 13:44:03 +00:00
parent 3d049204ed
commit 22abbc0edb
1 changed files with 1 additions and 1 deletions
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2
perl/liftOverVCF.pl
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@ -55,7 +55,7 @@ while ( $inHeader == 1 ) {
}
close(UNSORTED);
$cmd = "grep \"^#\" -v $unsorted_vcf | sort -n +1 -T $tmp | $gatk/perl/sortByRef.pl --tmp $tmp - $newRef.fasta.fai";
$cmd = "grep \"^#\" -v $unsorted_vcf | sort -n -k2 -T $tmp | $gatk/perl/sortByRef.pl --tmp $tmp - $newRef.fasta.fai";
print SORTED `$cmd`;
close(SORTED);