-
Notifications
You must be signed in to change notification settings - Fork 0
/
InHouse_MAF_fromVCFs_StructuralVariants.pl
220 lines (206 loc) · 8.78 KB
/
InHouse_MAF_fromVCFs_StructuralVariants.pl
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
#!/usr/bin/perl
use strict;
use warnings;
#define variables
my $Line;
my $file;
my %vars=();
my %contiglengths=();
my $count=0;
my $binlength=10000;
my($path1, $vcfsfile, $ID, $genesfile)=@ARGV;
#open each vcf file and add variants into %vars
open INPUT2, $vcfsfile or die "Cannot open $vcfsfile\n";
lineloop2: foreach $file (<INPUT2>){
chomp $file;
$count++;
open INPUT, $file or die "Cannot open $file\n";
lineloop: foreach $Line (<INPUT>){
chomp $Line;
##Store genome contig lengths
if($Line=~/\#\#contig\=\<ID\=(\S+?)\,length\=(d+?)\>/){
my $cont=$1;
my $totlength=$2;
if(!exists $contiglengths{$cont}){$contiglengths{$cont}=$totlength; print "Head\: $cont\t$totlength\n";}
next lineloop;
}#if head line matches contig name/ID
if($Line=~/^\#\#/){
next lineloop;
}#skip other header lines
my @linesplit2=split(/\t/,$Line); ##split information lines
if($Line=~/^\#CHROM/){
my $additionalIDs=(scalar(@linesplit2))-10;
$count+=$additionalIDs;
next lineloop;
}####CHROM header
my $chr=$linesplit2[0];
my $SVstartPOS=$linesplit2[1];
my $SVendPOS=$SVstartPOS;
my $SVtype="NA";
if($linesplit2[7]=~/END=(\d+?)\;/){$SVendPOS=$1;}
if($linesplit2[7]=~/SVTYPE=(\S+?)\;/){$SVtype=$1;}
if(!exists $contiglengths{$chr}){$contiglengths{$chr}=249000000; print "plus\: $chr\t249000000\n";}
#Populate %vars with each per 'bin' position represented by SV
if(!exists $vars{$chr}{$SVtype}){
for(my $bs=0; $bs<=$contiglengths{$chr}; $bs+=$binlength){
my $be=$bs+$binlength-1;
$vars{$chr}{$SVtype}{$bs}{$be}{'total'}=0;
$vars{$chr}{$SVtype}{$bs}{$be}{'hets'}=0;
$vars{$chr}{$SVtype}{$bs}{$be}{'homs'}=0;
$vars{$chr}{$SVtype}{$bs}{$be}{'gain'}=0;
$vars{$chr}{$SVtype}{$bs}{$be}{'loss'}=0;
}#for each bin
}#initialise each per chr/contig structural variant type in %vars
##Count up number of genotypes per bin
my $bsp=0;
for(my $p=$SVstartPOS;$p<=($SVendPOS+$binlength);$p+=$binlength){ #for each per 'bin' POS of SV
binloop: for(my $bs=$bsp; $bs<=$contiglengths{$chr}; $bs+=$binlength){
my $be=$bs+$binlength-1;
if($bs>$p){last binloop;}
if($be<($p+1)){$bsp=$bs; next binloop;}
if(($bs+1)<=$p and $p<=($be+1)){
$bsp=$bs;
##loop through each genotype
loop: for(my $i=9;$i<scalar(@linesplit2);$i++){
$vars{$chr}{$SVtype}{$bs}{$be}{'total'}+=2;
##Add gain or loss counts for e.g CNV or LOH calls
if($linesplit2[8]=~/^RC\:BC\:CN/){
my @fields=split(/\:/,$linesplit2[$i]);
if($fields[2]==2){next loop;}
if($fields[2]==0){$vars{$chr}{$SVtype}{$bs}{$be}{'loss'}+=2;}
if($fields[2]==1){$vars{$chr}{$SVtype}{$bs}{$be}{'loss'}+=1;}
if($fields[2]==3){$vars{$chr}{$SVtype}{$bs}{$be}{'gain'}+=1;}
if($fields[2]>=4){$vars{$chr}{$SVtype}{$bs}{$be}{'gain'}+=2;}
}
##Add gain or loss counts for e.g. CNV or LOH calls
if($linesplit2[8]=~/^GT\:RC\:BC\:CN/){
my @fields=split(/\:/,$linesplit2[$i]);
if($fields[3]==2){next loop;}
if($fields[3]==0){$vars{$chr}{$SVtype}{$bs}{$be}{'loss'}+=2;}
if($fields[3]==1){$vars{$chr}{$SVtype}{$bs}{$be}{'loss'}+=1;}
if($fields[3]==3){$vars{$chr}{$SVtype}{$bs}{$be}{'gain'}+=1;}
if($fields[3]>=4){$vars{$chr}{$SVtype}{$bs}{$be}{'gain'}+=2;}
}
if($linesplit2[$i]=~/0\/0/ or $linesplit2[$i]=~/\.\/\./){next loop;} #increment total called genotypes
if($linesplit2[$i]=~/([0123456789])\/([123456789])/){
my $first=$1;
my $second=$2;
if($first eq $second){
$vars{$chr}{$SVtype}{$bs}{$be}{'homs'}++;
next loop;
} #homozygote for variant ... ref genos 0/0 'looped' out line 39
if($first ne $second){
$vars{$chr}{$SVtype}{$bs}{$be}{'hets'}++;
next loop;
} #heterozygote
}# if genotype non-REF
}#for loop - genotypes
}##if $p within or equal to $bs and $be
}#for each bin
}#for each position + binsize increments
}#lineloop
print "$file\n";
close INPUT;
}#foreach vcf file
close INPUT2;
#open output file and print header
my %rarevars=();
my $output_file = $path1."/InHouse_MAFs_StructuralVariants_".$ID."_".$count."x_participants.txt";
open(OUT, ">>$output_file") || die "Cannot open file \"$output_file\" to write to!\n";
print OUT "\#CHROM\tPOS_BIN_START\tPOS_BIN_END\tSV_TYPE\tTOT_CALLED_GENOS\tHET\tHOM\tCN_LOSS\tCN_GAIN\tMAF_ALL\n";
foreach my $c (sort keys %vars){
foreach my $r (sort keys %{$vars{$c}}){
foreach my $sp (sort {$a<=>$b} keys %{$vars{$c}{$r}}){
foreach my $ep (sort {$a<=>$b} keys %{$vars{$c}{$r}{$sp}}){
my $maf="\.";
my $totalgenotypes=0;
my $count2=$count*2;
if($count2<$vars{$c}{$r}{$sp}{$ep}{'total'}){$count2=$vars{$c}{$r}{$sp}{$ep}{'total'};}
unless($vars{$c}{$r}{$sp}{$ep}{'total'}==0){
if(($r ne "CNV") and ($r ne "LOH")){$maf=($vars{$c}{$r}{$sp}{$ep}{'hets'}+(2*$vars{$c}{$r}{$sp}{$ep}{'homs'}))/$count2;}
if(($r eq "CNV") or ($r eq "LOH")){$maf=($vars{$c}{$r}{$sp}{$ep}{'loss'}+$vars{$c}{$r}{$sp}{$ep}{'gain'})/$count2;}
$totalgenotypes=$vars{$c}{$r}{$sp}{$ep}{'total'}/2;
#Add rare SV bin coordinates to %rarevars
if($maf<0.001){$rarevars{$c}{$r}{$sp}{$ep}=$maf;}
#Print cumulative InHouse SVs to file
print OUT "$c\t$sp\t$ep\t$r\t$totalgenotypes\t$vars{$c}{$r}{$sp}{$ep}{'hets'}\t$vars{$c}{$r}{$sp}{$ep}{'homs'}\t$vars{$c}{$r}{$sp}{$ep}{'loss'}\t$vars{$c}{$r}{$sp}{$ep}{'gain'}\t$maf\n";
}#unless total=0
}#per end pos
}#per start pos
}#per SV type
}#per chr
close OUT;
##Open candidate/selected genes file
my %candG=();
open INPUT3, $genesfile or die "Cannot open $genesfile\n";
lineloop3: foreach $Line (<INPUT3>){
chomp $Line;
$Line=~s/\"//g;
my @linesplit3=split(/\t/,$Line);
if(!exists $candG{$linesplit3[0]}{$linesplit3[1]}{$linesplit3[2]}){
$candG{$linesplit3[0]}{$linesplit3[1]}{$linesplit3[2]}=$linesplit3[3];
} ##Genesymbol=ls3;ENSGID=ls4
}
close INPUT3;
##Re-read through filtered SV files and Print rare SVs to total file
my $output_file2 = $path1."/Rare_StructuralVariants_".$ID."_".$count."x_participants.txt";
open(OUT2, ">>$output_file2") || die "Cannot open file \"$output_file2\" to write to!\n";
print OUT2 "Part_ID\tVariant\tGENOTYPE_CN\tGeneSymbol\tIHMAF\tPOPN\tCONSEQUENCE\tCHROM\tSTARTPOS\tENDPOS\tLENGTH\(Mb\)\n";
#open each vcf file and add variants into %vars
open INPUT2, $vcfsfile or die "Cannot open $vcfsfile\n";
lineloop2: foreach $file (<INPUT2>){
chomp $file;
open INPUT, $file or die "Cannot open $file\n";
my $ID="NA";
lineloop3: foreach $Line (<INPUT>){
chomp $Line;
if($Line=~/^\#\#/){
next lineloop3;
}#skip other header lines
my @linesplit2=split(/\t/,$Line); ##split information lines
if($Line=~/^\#CHROM/){
$ID=$linesplit2[9];
next lineloop3;
}####CHROM header
my $chr=$linesplit2[0];
my $SVstartPOS=$linesplit2[1];
my $SVendPOS=$SVstartPOS;
my $SVtype="NA";
if($linesplit2[7]=~/END=(\d+?)\;/){$SVendPOS=$1;}
if($linesplit2[7]=~/SVTYPE=(\S+?)\;/){$SVtype=$1;}
#Find if present within positional bins of %rarevars
if(!exists $rarevars{$chr}{$SVtype}){next lineloop3;}
#loop through each position of rare SVs per chr+type
my $genoCN=$linesplit2[9];
if($linesplit2[8]=~/^RC\:BC\:CN$/){$genoCN=~s/\d+\:\d+\:/CN/;}
if($linesplit2[8]=~/^RC\:BC\:CN\:MCC$/){$genoCN=~s/\d+\:\d+\:/CN/;$genoCN=~s/\:\d+//;}
if($linesplit2[8]=~/^GT/){$genoCN=~s/\:\S+//;}
foreach my $sp (sort {$a<=>$b} keys %{$rarevars{$chr}{$SVtype}}){
foreach my $ep (sort {$a<=>$b} keys %{$rarevars{$chr}{$SVtype}{$sp}}){
if(($sp<=$SVstartPOS and $ep>=$SVstartPOS) or ($sp<=$SVendPOS and $ep>=$SVendPOS) or ($sp>=$SVstartPOS and $ep<=$SVendPOS)){
##Add cand genes
my $CGenes=".";
if(exists $candG{$chr}){
foreach my $cst (keys %{$candG{$chr}}){
foreach my $ced (keys %{$candG{$chr}{$cst}}){
if(($cst<=$SVstartPOS and $ced>=$SVstartPOS) or ($cst<=$SVendPOS and $ced>=$SVendPOS) or ($cst>$SVstartPOS and $ced<$SVendPOS)){
$CGenes=$CGenes.", ".$candG{$chr}{$cst}{$ced};
}#if coords match to the structural variant - add genename to $CGenes
}#per gene end
}#per gene start
}#if chrom name in %CGenes
$CGenes=~s/\.\, //;
my $lengMB=($SVendPOS+1-$SVstartPOS)/1000000;
my $SVtype2=$SVtype;
if($SVtype=~/BND/){$SVtype2=$SVtype."_".$linesplit2[4];}
print OUT2 "$ID\t$chr\_$SVstartPOS\_$SVendPOS\_$lengMB\_Mb\t$genoCN\t$CGenes\t$rarevars{$chr}{$SVtype}{$sp}{$ep}\tInHouse$count\t$SVtype2\t$chr\t$SVstartPOS\t$SVendPOS\t$lengMB\n";
next lineloop3;
}#if matches within position bin
}#per end pos
}#per start pos
}#lineloop
close INPUT;
}#foreach vcf file
close INPUT2;
close OUT2;
exit;