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infer_sv.pl
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infer_sv.pl
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#!/usr/bin/perl -w
#
#Auther: Zechen Chong
#
use strict;
use warnings;
my @slines = ();
my @dlines = ();
my $id = 0;
print qq(##fileformat=VCFv4.1
##phasing=none
##INDIVIDUAL=TRUTH
##SAMPLE=<ID=TRUTH,Individual="TRUTH",Description="bamsurgeon spike-in">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variation">
##INFO=<ID=CT,Number=1,Type=String,Description="Paired-end signature induced connection type">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic mutation in primary">
##INFO=<ID=GERMLINE,Number=0,Type=Flag,Description="Germline structural variant">
##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for END coordinate in case of a translocation">
##INFO=<ID=UNKNOWN_LEN,Number=0,Type=Flag,Description="Unknown the length of SV">
##INFO=<ID=CONSENSUS,Number=1,Type=String,Description="Breakpoint consensus sequence">
##ALT=<ID=INV,Description="Inversion">
##ALT=<ID=DUP,Description="Duplication">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=INS,Description="Insertion">
##ALT=<ID=TRA,Description="Translocation">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SPIKEIN
);
my $pre = "";
my @results = ();
while (<>) {
next if /^@/;
my @e = split /\s+/, $_;
next if $e[1] == 4 or $e[5]!~/[SH]/;
my $newcigar = "";
my $match = 0;
while ($e[5] =~ /(\d+)([SMIDH])/g) {
my ($l, $t) = ($1, $2);
if ($t eq 'S' or $t eq 'H') {
if (!$match) {
$newcigar .= $l.$t;
} else {
$newcigar .= $match."M";
$newcigar .= $l.$t;
$match = 0;
}
}
$match += $l if $t eq 'M';
if ($t eq 'I' or $t eq 'D') {
if ($l > 20) { # TODO: magic number
$newcigar .= $match."M";
$newcigar .= $l.$t;
$match = 0;
} else {
$match += $l if $t eq 'I';
}
}
}
$newcigar .= $match."M" if $match;
$e[5] = $newcigar;
#if ($e[5] =~ /(\d+)[SH].+M(\d+)[SH]/) {
# next if ($1>5 and $2>5);
#}
if ($e[5] =~ /(\d+)M.+?(\d+)M/) {
next if ($1>10 and $2>10);
}
$_ = join("\t", @e);
if ($e[0] ne $pre) {
if ($pre ne "") {
if (@dlines >= 2) {
my $seq = &pick_consensus(@dlines);
for (my $i = 0; $i < scalar @dlines - 1; $i++) {
for (my $j = $i+1; $j < scalar @dlines; $j++) {
push @results, &parse_bp1($dlines[$i], $dlines[$j], $seq);
}
}
}
@dlines = ();
}
$pre = $e[0];
if ($e[5] =~ /(\d+)[SH].+M(\d+)[SH]/) {
my $tmp = $e[5];
if ($1 > 20) {
$e[5] =~ s/$2[SH]//;
$_ = join ("\t", @e);
push @dlines, $_;
$e[5] = $tmp;
}
if ($2 > 20) {
$e[5] =~ s/$1[SH]//;
$_ = join ("\t", @e);
push @dlines, $_;
}
$e[5] = $tmp;
} else {
push @dlines, $_;
}
} else {
if ($e[5] =~ /(\d+)[SH].+M(\d+)[SH]/) {
my $tmp = $e[5];
if ($1 > 20) {
$e[5] =~ s/$2[SH]//;
$_ = join ("\t", @e);
push @dlines, $_;
$e[5] = $tmp;
}
if ($2 > 20) {
$e[5] =~ s/$1[SH]//;
$_ = join ("\t", @e);
push @dlines, $_;
}
$e[5] = $tmp;
} else {
push @dlines, $_;
}
}
}
if (@dlines >= 2) {
my $seq = &pick_consensus(@dlines);
for (my $i = 0; $i < scalar @dlines - 1; $i++) {
for (my $j = $i+1; $j < scalar @dlines; $j++) {
push @results, &parse_bp1($dlines[$i], $dlines[$j], $seq);
}
}
}
@results = sort {$a->[0] cmp $b->[0] or $a->[1] <=> $b->[1]} @results;
my $prepos = 0;
for (my $i = 0; $i < @results; $i++) {
print join("\t", @{$results[$i]}), "\n";
}
1;
sub pick_consensus {
my @lines = @_;
foreach my $l (@lines) {
my @e = split /\s+/, $l;
next if $e[1] & 256;
return $e[9];
}
}
sub parse_ins {
my $l = shift;
my @lines = @$l;
my $seq = &pick_consensus(@lines);
my @bps = ();
my @ret = ();
for (my $i = 0; $i < @lines; $i++) {
my @e = split /\s+/, $lines[$i];
my ($m1, $s1) = (0, 0);
while ($e[5] =~ /(\d+)[SH]/g) {
$s1 = $1 if $1 > $s1;
}
while ($e[5] =~ /(\d+)M/g) {
$m1 = $1 if $1 > $m1;
}
if ($e[5] =~ /$m1[M].*?$s1[SH]/) {
$e[3] = $e[3]+$m1-1;
}
push @bps, [ ($e[2],$e[3],$e[1], $e[4],$e[5], $e[0]) ];
# print join("\t", $e[2],$e[3], $e[4], $e[5]), "\n";
}
@bps = sort {$a->[0] cmp $b->[0] or $a->[1] <=> $b->[1]} @bps;
# foreach (@bps) {
# my @rec = @$_;
# print join("\t", @rec), "\n";
# }
my @pre = ();
my @cur = ();
foreach (@bps) {
@cur = @$_;
if (@pre) {
if ($cur[0] eq $pre[0] and $cur[1]-$pre[1]<3) { #TODO magic number
#print join("\t", $pre[0],$pre[1], $pre[2], $pre[3], $pre[4]), "\n";
#print join("\t", $cur[0],$cur[1], $cur[2], $cur[3], $cur[4]), "\n";
my ($m1, $s1, $m2, $s2) = (0, 0, 0, 0);
while ($pre[4] =~ /(\d+)[SH]/g) {
$s1 = $1 if $1 > $s1;
}
while ($pre[4] =~ /(\d+)M/g) {
$m1 = $1 if $1 > $m1;
}
while ($cur[4] =~ /(\d+)[SH]/g) {
$s2 = $1 if $1 > $s2;
}
while ($cur[4] =~ /(\d+)M/g) {
$m2 = $1 if $1 > $m2;
}
#print "MS", $m1, "\t", $s1, "\t", $m2, "\t", $s2, "\n";
if (($pre[4]=~/$m1[M].*?$s1[SH]/ and $cur[4]=~/$s2[SH].*?$m2[M]/) or ($pre[4]=~/$s1[SH].*?$m1[M]/ and $cur[4]=~/$m2[M].*?$s2[SH]/)) {
if (($pre[2]&16 and $cur[2]&16) or (!($pre[2]&16) and !($cur[2]&16))) { # same strand
#print join("\t", $cur[0], $pre[1], ".", ".", "<INS>", ($pre[3]+$cur[3])/2, "PASS", "PRECISE;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=$seq;SVTYPE=INS;END=$cur[1];SVLEN=".($cur[1]-$pre[1]), "GT", "./."), "\n";
push @ret, [ ($cur[0], $pre[1], "N", ".", "<INS>", ($pre[3]+$cur[3])/2, "PASS", "PRECISE;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=$seq;SVTYPE=INS;CHR2=$cur[0];END=$cur[1];UNKNOWN_LEN;SVLEN=".($cur[1]-$pre[1]), "GT", "./.", $cur[-1]) ];
}
}
if (($pre[4]=~/$m1[M].*?$s1[SH]/ and $cur[4]=~/$m2[M].*?$s2[SH]/) or ($pre[4]=~/$s1[SH].*?$m1[M]/ and $cur[4]=~/$s2[SH].*?$m2[M]/)) {
if (($pre[2]&16 and !($cur[2]&16)) or (!($pre[2]&16) and $cur[2]&16)) { # different strand
#print join("\t", $cur[0], $pre[1], ".", ".", "<INS>", ($pre[3]+$cur[3])/2, "PASS", "PRECISE;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=$seq;SVTYPE=INS;END=$cur[1];SVLEN=".($cur[1]-$pre[1]), "GT", "./."), "\n";
push @ret, [ ($cur[0], $pre[1], "N", ".", "<INS>", ($pre[3]+$cur[3])/2, "PASS", "PRECISE;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=$seq;SVTYPE=INS;CHR2=$cur[0];END=$cur[1];UNKNOWN_LEN;SVLEN=".($cur[1]-$pre[1]), "GT", "./.", $cur[-1]) ];
}
}
}
@pre = @cur;
} else {
@pre = @cur;
}
#print join("\t", $_->[0],$_->[1], $_->[2], $_->[3], $_->[4]), "\n";
}
#print @bps;
return @ret;
}
sub parse_bp1 {
my $line1 = shift;
my $line2 = shift;
my $seq = shift;
my @ret = ();
my ($m1, $s1, $m2, $s2) = (0, 0, 0, 0);
my @e1 = split /\s+/, $line1;
my @e2 = split /\s+/, $line2;
if ($e1[5] =~ /[SMH]/ and $e2[5] =~ /[SMH]/) {
while ($e1[5] =~ /(\d+)[SH]/g) {
$s1 = $1 if $1 > $s1;
}
while ($e1[5] =~ /(\d+)M/g) {
$m1 = $1 if $1 > $m1;
}
while ($e2[5] =~ /(\d+)[SH]/g) {
$s2 = $1 if $1 > $s2;
}
while ($e2[5] =~ /(\d+)M/g) {
$m2 = $1 if $1 > $m2;
}
}
my ($pos1, $pos2) = (0, 0);
if ($e1[5] =~ /$s1[SH].*?$m1[M]/) {
$pos1 = $e1[3];
} else {
$pos1 = $e1[3]+$m1-1;
}
if ($e2[5] =~ /$s2[SH].*?$m2[M]/) {
$pos2 = $e2[3];
} else {
$pos2 = $e2[3]+$m2-1;
}
if (abs($m1-$s2)<=25 or abs($m2-$s1)<=25) {
if ($e1[2] ne $e2[2]) { # trans
if ((($e1[1] & 0x10) ^ ($e2[1] & 0x10)) == 0) { # +,+ or -,-
if ($e1[1] & 0x10) { #minus
if ($pos1 == $e1[3]) {
push @ret, [ ($e1[2], $pos1, "N", ".", "<TRA>", ($e1[4]+$e2[4])/2, "PASS", "PRECISE;CT=5to3;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=$seq;SVTYPE=TRA;CHR2=$e2[2];END=$pos2;SVLEN=0", "GT", "./.", $e1[0]) ];
}
if ($pos2 == $e2[3]) {
push @ret, [ ($e2[2], $pos2, "N", ".", "<TRA>", ($e1[4]+$e2[4])/2, "PASS", "PRECISE;CT=5to3;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=$seq;SVTYPE=TRA;CHR2=$e1[2];END=$pos1;SVLEN=0", "GT", "./.", $e2[0]) ];
}
} else { #plus
if ($pos2 == $e2[3]) {
push @ret, [ ($e1[2], $pos1, "N", ".", "<TRA>", ($e1[4]+$e2[4])/2, "PASS", "PRECISE;CT=3to5;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=$seq;SVTYPE=TRA;CHR2=$e2[2];END=$pos2;SVLEN=0", "GT", "./.", $e1[0]) ];
}
if ($pos1 == $e1[3]) {
push @ret, [ ($e2[2], $pos2, "N", ".", "<TRA>", ($e1[4]+$e2[4])/2, "PASS", "PRECISE;CT=3to5;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=$seq;SVTYPE=TRA;CHR2=$e1[2];END=$pos1;SVLEN=0", "GT", "./.", $e2[0]) ];
}
}
} else { # +,- or -,+
if ($e1[1] & 0x10) {
if ($pos1 == $e1[3]) {
push @ret, [ ($e1[2], $pos1, "N", ".", "<TRA>", ($e1[4]+$e2[4])/2, "PASS", "PRECISE;CT=5to5;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=$seq;SVTYPE=TRA;CHR2=$e2[2];END=$pos2;SVLEN=0", "GT", "./.", $e1[0]) ];
} else {
push @ret, [ ($e2[2], $pos2, "N", ".", "<TRA>", ($e1[4]+$e2[4])/2, "PASS", "PRECISE;CT=3to3;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=$seq;SVTYPE=TRA;CHR2=$e1[2];END=$pos1;SVLEN=0", "GT", "./.", $e2[0]) ];
}
} else {
if ($pos1 == $e1[3]) {
push @ret, [ ($e2[2], $pos2, "N", ".", "<TRA>", ($e1[4]+$e2[4])/2, "PASS", "PRECISE;CT=5to5;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=$seq;SVTYPE=TRA;CHR2=$e1[2];END=$pos1;SVLEN=0", "GT", "./.", $e2[0]) ];
} else {
push @ret, [ ($e1[2], $pos1, "N", ".", "<TRA>", ($e1[4]+$e2[4])/2, "PASS", "PRECISE;CT=3to3;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=$seq;SVTYPE=TRA;CHR2=$e2[2];END=$pos2;SVLEN=0", "GT", "./.", $e1[0]) ];
}
}
}
} else {
if ((($e1[1] & 16) and !($e2[1] & 16)) or (!($e1[1] & 16)) and ($e2[1] & 16)) { # inv
if(abs($pos2 - $pos1) < 10) { # TODO magic number controling inv size
}
else {
if ($pos1 < $pos2) {
#print join("\t", $e2[2], $pos1, ".", ".", "<INV>", ($e1[4]+$e2[4])/2, "PASS", "PRECISE;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=$seq;SVTYPE=INV;END=$pos2;SVLEN=0", "GT", "./."), "\n";
push @ret, [ ($e2[2], $pos1, "N", ".", "<INV>", ($e1[4]+$e2[4])/2, "PASS", "PRECISE;CT=5to5;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=$seq;SVTYPE=INV;CHR2=$e2[2];END=$pos2;SVLEN=".abs($pos2-$pos1+1), "GT", "./.",$e2[0]) ] ;
} else {
#print join("\t", $e2[2], $pos2, ".", ".", "<INV>", ($e1[4]+$e2[4])/2, "PASS", "PRECISE;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=$seq;SVTYPE=INV;END=$pos1;SVLEN=0", "GT", "./."), "\n";
push @ret, [ ($e2[2], $pos2, "N", ".", "<INV>", ($e1[4]+$e2[4])/2, "PASS", "PRECISE;CT=3to3;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=$seq;SVTYPE=INV;CHR2=$e2[2];END=$pos1;SVLEN=".abs($pos2-$pos1+1), "GT", "./.",$e2[0]) ];
}
}
} else {
#print $line1, $line2;
if ($pos1 < $pos2) {
if ((!($e1[1]&16) and $e1[5]=~/$m1[M].*?$s1[SH]/) or ($e1[1]&16 and $e1[5]=~/$s1[SH].*?$m1[M]/)) { # del
#print join("\t", $e2[2], $pos1, ".", ".", "<DEL>", ($e1[4]+$e2[4])/2, "PASS", "PRECISE;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=$seq;SVTYPE=DEL;END=$pos2;SVLEN=".($pos1-$pos2), "GT", "./."), "\n";
if(abs($pos2 - $pos1) > 10) { # TODO magic number controling del size
push @ret, [ ($e2[2], $pos1, "N", ".", "<DEL>", ($e1[4]+$e2[4])/2, "PASS", "PRECISE;CT=3to5;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=$seq;SVTYPE=DEL;CHR2=$e2[2];END=$pos2;SVLEN=".($pos1-$pos2), "GT", "./.",$e2[0])] ;
}
} else { # dup
#print join("\t", $e2[2], $pos1, ".", ".", "<DUP>", ($e1[4]+$e2[4])/2, "PASS", "PRECISE;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=$seq;SVTYPE=DUP;END=$pos2;SVLEN=".($pos2-$pos1), "GT", "./."), "\n";
push @ret, [ ($e2[2], $pos1, "N", ".", "<DUP>", ($e1[4]+$e2[4])/2, "PASS", "PRECISE;CT=5to3;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=$seq;SVTYPE=DUP;CHR2=$e2[2];END=$pos2;SVLEN=".($pos2-$pos1), "GT", "./.",$e2[0]) ];
}
} else {
if ((!($e2[1]&16) and $e2[5]=~/$m2[M].*?$s2[SH]/) or ($e2[1]&16 and $e2[5]=~/$s2[SH].*?$m2[M]/)) { # del
#print join("\t", $e2[2], $pos2, ".", ".", "<DEL>", ($e1[4]+$e2[4])/2, "PASS", "PRECISE;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=$seq;SVTYPE=DEL;END=$pos1;SVLEN=".($pos2-$pos1), "GT", "./."), "\n";
if(abs($pos2 - $pos1) > 10) { # TODO magic number controling del size
push @ret, [ ($e2[2], $pos2, "N", ".", "<DEL>", ($e1[4]+$e2[4])/2, "PASS", "PRECISE;CT=3to5;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=$seq;SVTYPE=DEL;CHR2=$e2[2];END=$pos1;SVLEN=".($pos2-$pos1), "GT", "./.",$e2[0]) ];
}
} else { # dup
#print join("\t", $e2[2], $pos2, ".", ".", "<DUP>", ($e1[4]+$e2[4])/2, "PASS", "PRECISE;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=$seq;SVTYPE=DUP;END=$pos1;SVLEN=".($pos1-$pos2), "GT", "./."), "\n";
push @ret, [ ($e2[2], $pos2, "N", ".", "<DUP>", ($e1[4]+$e2[4])/2, "PASS", "PRECISE;CT=5to3;CIPOS=-10,10;CIEND=-10,10;SOMATIC;CONSENSUS=$seq;SVTYPE=DUP;CHR2=$e2[2];END=$pos1;SVLEN=".($pos1-$pos2), "GT", "./.",$e2[0]) ];
}
}
}
}
}
return @ret;
}