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filter_sv.pl
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filter_sv.pl
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#!/usr/bin/perl -w
#
use strict;
use warnings;
while (<>) {
my @e = split;
my $len = abs $1 if /SVLEN=(\S+)/;
if ($len < 1000 and $len > 100 and $e[18] + $e[28] > 2 and $e[21] < 2 and $e[31] < 2 and $e[13] > 3 and $e[5] > 10) { # small svs
print;
}
#elsif ($e[35]>=2 and $e[36]/$e[35] < 0.1 and $e[37]>=2 and $e[38]/$e[37] < 0.1 or ($e[35]<=1 and $e[37]<=1 and $e[13]>2 and $e[23]<2 and $e[33]<2 and $e[18]+$e[28]>2)) { # this may be a better filter for real data
elsif (!/TRA/ and $e[36] <= 1 and $e[38] <= 1 and $e[23] <= 1 and $e[33] <= 1) {
if (!/TRA/ and $e[5]>=5) {
if (!/DUP/) {
if ($len > 100000) {
print if $e[5] > 50 or ($e[35]>5 and $e[37]>5);
} else {
print;
}
} else {
print;
}
}
} elsif (/TRA/) {
#if ($e[5] >= 30 and $e[13]>=3) {
my $end = $e[1]+1;
$e[7] =~ s/END=(\d+);/END=$end;/;
$e[7] =~ s/CHR2=(\S+?);/CHR2=$e[0];/;
$e[7] =~ s/TRA/INS/;
$e[4] =~ s/TRA/INS/;
$e[37] = $e[35];
$e[38] = $e[36];
splice @e, 25, 10, @e[15..24];
print join("\t", @e), "\n";
#}
#if ($e[5] >= 30 and $e[13]>=3) {
@e = split;
my $chr2 = $1 if /CHR2=(\S+?);/;
my $end2 = $1 if /END=(\d+);/;
$e[0] = $chr2;
$e[1] = $end2-1;
$e[7] =~ s/TRA/INS/;
$e[4] =~ s/TRA/INS/;
$e[35] = $e[37];
$e[36] = $e[38];
splice @e, 15, 10, @e[25..34];
print join("\t", @e), "\n";
#}
}
}