exit;
sub main {
- my $version = '0.1.0';
&usage if (@ARGV < 1);
my $command = shift(@ARGV);
my %func = (subsam=>\&subsam, listsam=>\&listsam, fillac=>\&fillac, qstats=>\&qstats, varFilter=>\&varFilter,
- hapmap2vcf=>\&hapmap2vcf, ucscsnp2vcf=>\&ucscsnp2vcf);
+ hapmap2vcf=>\&hapmap2vcf, ucscsnp2vcf=>\&ucscsnp2vcf, filter4vcf=>\&varFilter, ldstats=>\&ldstats,
+ gapstats=>\&gapstats);
die("Unknown command \"$command\".\n") if (!defined($func{$command}));
&{$func{$command}};
}
}
}
+sub ldstats {
+ my %opts = (t=>0.9);
+ getopts('t:', \%opts);
+ die("Usage: vcfutils.pl ldstats [-t $opts{t}] <in.vcf>\n") if (@ARGV == 0 && -t STDIN);
+ my $cutoff = $opts{t};
+ my ($last, $lastchr) = (0x7fffffff, '');
+ my ($x, $y, $n) = (0, 0, 0);
+ while (<>) {
+ if (/^([^#\s]+)\s(\d+)/) {
+ my ($chr, $pos) = ($1, $2);
+ if (/NEIR=([\d\.]+)/) {
+ ++$n;
+ ++$y, $x += $pos - $last if ($lastchr eq $chr && $pos > $last && $1 > $cutoff);
+ }
+ $last = $pos; $lastchr = $chr;
+ }
+ }
+ print "Number of SNP intervals in strong LD (r > $opts{t}): $y\n";
+ print "Fraction: ", $y/$n, "\n";
+ print "Length: $x\n";
+}
+
sub qstats {
my %opts = (r=>'', s=>0.02, v=>undef);
getopts('r:s:v', \%opts);
next if (length($t[3]) != 1 || uc($t[3]) eq 'N');
$t[3] = uc($t[3]); $t[4] = uc($t[4]);
my @s = split(',', $t[4]);
- $t[5] = 3 if ($t[5] < 0);
+ $t[5] = 3 if ($t[5] eq '.' || $t[5] < 0);
next if (length($s[0]) != 1);
my $hit;
if ($is_vcf) {
}
sub varFilter {
- my %opts = (d=>1, D=>10000, l=>30, Q=>25, q=>10, G=>25, s=>100, w=>10, W=>10, N=>2, p=>undef, F=>.001);
- getopts('pq:d:D:l:Q:w:W:N:G:F:', \%opts);
+ my %opts = (d=>2, D=>10000, a=>2, W=>10, Q=>10, w=>10, p=>undef, 1=>1e-4, 2=>1e-100, 3=>0, 4=>1e-4);
+ getopts('pd:D:W:Q:w:a:1:2:3:4:', \%opts);
die(qq/
Usage: vcfutils.pl varFilter [options] <in.vcf>
Options: -Q INT minimum RMS mapping quality for SNPs [$opts{Q}]
- -q INT minimum RMS mapping quality for gaps [$opts{q}]
-d INT minimum read depth [$opts{d}]
-D INT maximum read depth [$opts{D}]
-
- -G INT min indel score for nearby SNP filtering [$opts{G}]
+ -a INT minimum number of alternate bases [$opts{a}]
-w INT SNP within INT bp around a gap to be filtered [$opts{w}]
-
- -W INT window size for filtering dense SNPs [$opts{W}]
- -N INT max number of SNPs in a window [$opts{N}]
-
- -l INT window size for filtering adjacent gaps [$opts{l}]
-
+ -W INT window size for filtering adjacent gaps [$opts{W}]
+ -1 FLOAT min P-value for strand bias (given PV4) [$opts{1}]
+ -2 FLOAT min P-value for baseQ bias [$opts{2}]
+ -3 FLOAT min P-value for mapQ bias [$opts{3}]
+ -4 FLOAT min P-value for end distance bias [$opts{4}]
-p print filtered variants
+
+Note: Some of the filters rely on annotations generated by SAMtools\/BCFtools.
\n/) if (@ARGV == 0 && -t STDIN);
# calculate the window size
- my ($ol, $ow, $oW) = ($opts{l}, $opts{w}, $opts{W});
+ my ($ol, $ow) = ($opts{W}, $opts{w});
my $max_dist = $ol > $ow? $ol : $ow;
- $max_dist = $oW if ($max_dist < $oW);
# the core loop
- my @staging; # (indel_filtering_score, flt_tag)
+ my @staging; # (indel_filtering_score, flt_tag, indel_span; chr, pos, ...)
while (<>) {
my @t = split;
- next if (/^#/);
+ if (/^#/) {
+ print; next;
+ }
next if ($t[4] eq '.'); # skip non-var sites
+ # check if the site is a SNP
my $is_snp = 1;
if (length($t[3]) > 1) {
$is_snp = 0;
last if ($staging[0][3] eq $t[0] && $staging[0][4] + $staging[0][2] + $max_dist >= $t[1]);
varFilter_aux(shift(@staging), $opts{p}); # calling a function is a bit slower, not much
}
- my ($flt, $score) = (0, -1);
-
- # collect key annotations
- my ($dp, $mq, $af) = (-1, -1, 1);
- if ($t[7] =~ /DP=(\d+)/i) {
- $dp = $1;
- } elsif ($t[7] =~ /DP4=(\d+),(\d+),(\d+),(\d+)/i) {
+ my $flt = 0;
+ # parse annotations
+ my ($dp, $mq, $dp_alt) = (-1, -1, -1);
+ if ($t[7] =~ /DP4=(\d+),(\d+),(\d+),(\d+)/i) {
$dp = $1 + $2 + $3 + $4;
+ $dp_alt = $3 + $4;
}
- if ($t[7] =~ /MQ=(\d+)/i) {
- $mq = $1;
- }
- if ($t[7] =~ /AF=([^\s;=]+)/i) {
- $af = $1;
- } elsif ($t[7] =~ /AF1=([^\s;=]+)/i) {
- $af = $1;
+ if ($t[7] =~ /DP=(\d+)/i) {
+ $dp = $1;
}
- # the depth filter
+ $mq = $1 if ($t[7] =~ /MQ=(\d+)/i);
+ # the depth and mapQ filter
if ($dp >= 0) {
if ($dp < $opts{d}) {
$flt = 2;
$flt = 3;
}
}
+ $flt = 4 if ($dp_alt >= 0 && $dp_alt < $opts{a});
+ $flt = 1 if ($flt == 0 && $mq >= 0 && $mq < $opts{Q});
+ $flt = 7 if ($flt == 0 && /PV4=([^,]+),([^,]+),([^,]+),([^,;\t]+)/
+ && ($1<$opts{1} || $2<$opts{2} || $3<$opts{3} || $4<$opts{4}));
# site dependent filters
- my $dlen = 0;
+ my ($rlen, $indel_score) = (0, -1); # $indel_score<0 for SNPs
if ($flt == 0) {
if (!$is_snp) { # an indel
- # If deletion, remember the length of the deletion
- $dlen = length($t[3]) - 1;
- $flt = 1 if ($mq < $opts{q});
+ $rlen = length($t[3]) - 1;
+ $indel_score = $t[5] * 100 + $dp_alt;
# filtering SNPs
- if ($t[5] >= $opts{G}) {
- for my $x (@staging) {
- # Is it a SNP and is it outside the SNP filter window?
- next if ($x->[0] >= 0 || $x->[4] + $x->[2] + $ow < $t[1]);
- $x->[1] = 5 if ($x->[1] == 0);
- }
+ for my $x (@staging) {
+ next if ($x->[0] >= 0 || $x->[1] || $x->[4] + $x->[2] + $ow < $t[1]);
+ $x->[1] = 5;
}
- # the indel filtering score
- $score = $t[5];
# check the staging list for indel filtering
for my $x (@staging) {
- # Is it a SNP and is it outside the gap filter window
- next if ($x->[0] < 0 || $x->[4] + $x->[2] + $ol < $t[1]);
- if ($x->[0] < $score) {
+ next if ($x->[0] < 0 || $x->[1] || $x->[4] + $x->[2] + $ol < $t[1]);
+ if ($x->[0] < $indel_score) {
$x->[1] = 6;
} else {
$flt = 6; last;
}
}
} else { # a SNP
- $flt = 1 if ($mq < $opts{Q});
- # check adjacent SNPs
- my $k = 1;
for my $x (@staging) {
- ++$k if ($x->[0] < 0 && -($x->[0] + 1) > $opts{F} && $x->[4] + $x->[2] + $oW >= $t[1] && ($x->[1] == 0 || $x->[1] == 4 || $x->[1] == 5));
- }
- # filtering is necessary
- if ($k > $opts{N}) {
- $flt = 4;
- for my $x (@staging) {
- $x->[1] = 4 if ($x->[0] < 0 && $x->[4] + $x->[2] + $oW >= $t[1] && $x->[1] == 0);
- }
- } else { # then check gap filter
- for my $x (@staging) {
- next if ($x->[0] < 0 || $x->[4] + $x->[2] + $ow < $t[1]);
- if ($x->[0] >= $opts{G}) {
- $flt = 5; last;
- }
- }
+ next if ($x->[0] < 0 || $x->[1] || $x->[4] + $x->[2] + $ow < $t[1]);
+ $flt = 5;
+ last;
}
}
}
- push(@staging, [$score < 0? -$af-1 : $score, $flt, $dlen, @t]);
+ push(@staging, [$indel_score, $flt, $rlen, @t]);
}
# output the last few elements in the staging list
while (@staging) {
if ($first->[1] == 0) {
print join("\t", @$first[3 .. @$first-1]), "\n";
} elsif ($is_print) {
- print STDERR join("\t", substr("UQdDWGgsiX", $first->[1], 1), @$first[3 .. @$first-1]), "\n";
+ print STDERR join("\t", substr("UQdDaGgP", $first->[1], 1), @$first[3 .. @$first-1]), "\n";
+ }
+}
+
+sub gapstats {
+ my (@c0, @c1);
+ $c0[$_] = $c1[$_] = 0 for (0 .. 10000);
+ while (<>) {
+ next if (/^#/);
+ my @t = split;
+ next if (length($t[3]) == 1 && $t[4] =~ /^[A-Za-z](,[A-Za-z])*$/); # not an indel
+ my @s = split(',', $t[4]);
+ for my $x (@s) {
+ my $l = length($x) - length($t[3]) + 5000;
+ if ($x =~ /^-/) {
+ $l = -(length($x) - 1) + 5000;
+ } elsif ($x =~ /^\+/) {
+ $l = length($x) - 1 + 5000;
+ }
+ $c0[$l] += 1 / @s;
+ }
+ }
+ for (my $i = 0; $i < 10000; ++$i) {
+ next if ($c0[$i] == 0);
+ $c1[0] += $c0[$i];
+ $c1[1] += $c0[$i] if (($i-5000)%3 == 0);
+ printf("C\t%d\t%.2f\n", ($i-5000), $c0[$i]);
}
+ printf("3\t%d\t%d\t%.3f\n", $c1[0], $c1[1], $c1[1]/$c1[0]);
}
sub ucscsnp2vcf {
projects / samtools.git / blobdiff