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comparison 2.4/script/Bam2pair.pl @ 13:e3609c8714fb draft

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author plus91-technologies-pvt-ltd
date Fri, 30 May 2014 03:37:55 -0400
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12:980fce54e60a 13:e3609c8714fb
1 #!/usr/bin/perl
2 #Author Steven Hart, PhD
3 #11-15-2012
4 #Convert and filter BAM files into merged bed
5 #Output should be
6 #chrA StartA EndA chrB StartB EndB Gene_id #supportingReads StrandA StrandB
7 #chr9 1000 5000 chr9 3000 3800 bedpe_example2 100 - +
8
9 use Cwd;
10 use File::Basename;
11 #Usage
12 sub usage(){
13 print "Usage: perl Bam2Pair.pl -b <BAM> -o <outfile>\n
14 -isize [10000]\t\tThe insert size to be considered discordant\n
15 -winsize [10000]\tThe distance between mate pairs to be considered the same\n
16 -min [1]\t\tThe minimum number of reads required to support an SV event\n
17 -prefix need a random prefix so files with the same name don't get created\n\n"
18 ;
19 }
20 $bedtools=`which intersectBed`;
21 $samtools=`which samtools`;
22
23 if(!defined($bedtools)){die "BEDtools must be installed\n";}
24 if(!defined($samtools)){die "Samtools must be installed\n";}
25 use Getopt::Long;
26 #Declare variables
27 GetOptions(
28 'b=s' => \$BAM_FILE, #path to bam
29 'out=s' => \$outfile, #path to output
30 'java:s' => \$java ,
31 'chrom:s' => \$chrom ,
32 'isize=i' => \$isize,
33 'winsize=i' => \$winsize,
34 'prefix=s' => \$prefix,
35 'min=i' => \$minSupport,
36 'blacklist:s' => \$new_blacklist,
37 'q=s' => \$qual,
38 'v' => \$verbose
39 );
40 #if(defined($picard_path)){$picard_path=$picard_path} else {die "Must specify a path to PICARD so that files can be sorted and indexed properly\n"};
41 if(!defined($BAM_FILE)){die "Must specify a BAM file!\n".usage();}
42 if(!defined($outfile)){die "Must specify an out filename!\n".usage();}
43 if(!defined($java)){$java=$java;}else{$java=`which java`}
44 if(!defined($qual)){$qual=20}
45 if($new_blacklist){$new_blacklist=" -L $new_blacklist"}
46
47
48 $Filter_BAM=$BAM_FILE;
49
50 @bam=split("/",$Filter_BAM);
51 $Filter_BAM=@bam[@bam-1];
52 $Filter_BAM=~s/.bam/$prefix.bam/;
53 $Filter_sam=$Filter_BAM;
54 $Filter_sam=~s/.bam/.sam/;
55
56
57
58
59 print "\nLooking for Discordant read pairs (and Unmated reads) without soft-clips\n";
60
61 #$command=join("","samtools view -h -q 20 -f 1 -F 1804 ",$BAM_FILE," ",$chrom," ",$new_blacklist," | awk -F\'\\t\' \'{if (\$9 > ", $isize, " || \$9 < -",$isize," || \$9 == 0 || \$1 ~ /^@/) print \$0}' > ",$Filter_sam);
62
63
64 #Change command to allow reads where mate is unmapped & remove qual
65 $command=join("","samtools view -h -f 1 -F 1800 -q $qual ",$BAM_FILE," ",$chrom," ",$new_blacklist," | awk -F\'\\t\' \'{if (\$9 > ", $isize, " || \$9 < -",$isize," || \$9 == 0 || \$1 ~ /^@/) print \$0}' > ",$Filter_sam);
66
67 print "$command\n" if ($verbose);
68 system($command);
69 $path = dirname(__FILE__);
70 $Filter_cluster=$Filter_sam;
71 $Filter_cluster=~s/.sam/.cluster/;
72 $command=join("",$path,"/ReadCluster.pl -i=$Filter_sam -o=$Filter_cluster -m $minSupport");
73 if($verbose){print "\n$command\n"};
74
75 system($command);
76
77 ##################################
78 #Now there are 2 SAM files of filtered reads
79 #.filter.cluster.inter.sam
80 #.filter.cluster.intra.sam
81 $result_pe=join("",$Filter_cluster,".out");
82 $command=join("","cat ",$Filter_cluster,".int\*|perl -ane 'next if(\@F[0]=~/^\@/);if(\@F[6]!~/=/){print join(\"\\t\",\$F[11],\@F[2],\@F[3],\@F[6],\@F[7],\"\\n\")}else{print join(\"\\t\",\$F[11],\@F[2],\@F[3],\@F[2],\@F[7],\"\\n\")}' >",$result_pe);
83 if($verbose){print $command."\n"};
84 system($command);
85 #my ($sample, $chrstart, $start, $chrend, $end)
86 $command=join("","cat ",$result_pe," | ",$path,"/cluster.pair.pl ",$winsize," |awk '(\$6 >",$minSupport,")' >> ", $outfile);
87 if($verbose){print $command."\n"};
88 system($command);
89 $filt1=join("",$Filter_cluster,".inter.sam");
90 $filt2=join("",$Filter_cluster,".intra.sam");
91
92
93 unlink($Filter_sam,$filt1,$filt2,$result_pe);
94
95 #########################################
96 #Now determine if left or righ clipping surrogate
97 print "\nBam2pair.pl Done\n";
98