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comparison snpEff_2_1a/scripts/sift2vcf.pl @ 0:f8eaa3f8194b default tip

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Uploaded snpEff_v2_1a_core.tgz from Pablo Cingolani
author greg
date Fri, 20 Apr 2012 14:47:09 -0400
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1 #!/usr/bin/perl
2
3
4 print "##INFO=<ID=SIFT_SCORE,Number=1,Type=Float,Description=\"SIFT score, 0 = Damaging, 1=Tolerated\">\n";
5 print "##INFO=<ID=SIFT_CONS,Number=1,Type=Float,Description=\"SIFT median conservation value, as log2. 0=High confidence, 4.32=Low confidence\">\n";
6 print "##INFO=<ID=SIFT_SEQS,Number=1,Type=Integer,Description=\"SIFT number of sequences at position\">\n";
7 print "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n";
8
9 while( $l = <STDIN> ) {
10 chomp $l;
11 ($chr, $coord1, $nt1, $nt2, $score, $median, $seqs_rep) = split /\t/, $l;
12
13 # Trim spaces
14 if( $seqs_rep =~ /\s(.*)/ ) { $seqs_rep = $1; }
15
16 $coord1++; # Get it in one-based coordinates
17
18 print "$chr\t$coord1\t.\t$nt1\t$nt2\t.\t.\tSIFT_SCORE=$score;SIFT_CONS=$median;SIFT_SEQS=$seqs_rep\n";
19 }