exit;
sub main {
- my $version = '0.1.0';
&usage if (@ARGV < 1);
my $command = shift(@ARGV);
my %func = (subsam=>\&subsam, listsam=>\&listsam, fillac=>\&fillac, qstats=>\&qstats, varFilter=>\&varFilter,
- hapmap2vcf=>\&hapmap2vcf);
+ hapmap2vcf=>\&hapmap2vcf, ucscsnp2vcf=>\&ucscsnp2vcf, filter4vcf=>\&varFilter, ldstats=>\&ldstats);
die("Unknown command \"$command\".\n") if (!defined($func{$command}));
&{$func{$command}};
}
print;
} else {
my @t = split;
- my @c;
+ my @c = (0);
my $n = 0;
- $c[1] = 0;
+ my $s = -1;
+ @_ = split(":", $t[8]);
+ for (0 .. $#_) {
+ if ($_[$_] eq 'GT') { $s = $_; last; }
+ }
+ if ($s < 0) {
+ print join("\t", @t), "\n";
+ next;
+ }
for (9 .. $#t) {
- if ($t[$_] =~ /^(\d+).(\d+)/) {
- ++$c[$1]; ++$c[$2];
+ if ($t[$_] =~ /^0,0,0/) {
+ } elsif ($t[$_] =~ /^([^\s:]+:){$s}(\d+).(\d+)/) {
+ ++$c[$2]; ++$c[$3];
$n += 2;
}
}
}
}
+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=>0.01);
- getopts('r:s:', \%opts);
+ my %opts = (r=>'', s=>0.02, v=>undef);
+ getopts('r:s:v', \%opts);
die("Usage: vcfutils.pl qstats [-r ref.vcf] <in.vcf>\n
Note: This command discards indels. Output: QUAL #non-indel #SNPs #transitions #joint ts/tv #joint/#ref #joint/#non-indel \n") if (@ARGV == 0 && -t STDIN);
my %ts = (AG=>1, GA=>1, CT=>1, TC=>1);
my %h = ();
+ my $is_vcf = defined($opts{v})? 1 : 0;
if ($opts{r}) { # read the reference positions
my $fh;
open($fh, $opts{r}) || die;
while (<$fh>) {
next if (/^#/);
- $h{$1,$2} = 1 if (/^(\S+)\s+(\d+)/);
+ if ($is_vcf) {
+ my @t = split;
+ $h{$t[0],$t[1]} = $t[4];
+ } else {
+ $h{$1,$2} = 1 if (/^(\S+)\s+(\d+)/);
+ }
}
close($fh);
}
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);
- push(@a, [$t[5], ($t[4] eq '.' || $t[4] eq $t[3])? 0 : 1, $ts{$t[3].$s[0]}? 1 : 0, $h{$t[0],$t[1]}? 1 : 0]);
+ my $hit;
+ if ($is_vcf) {
+ $hit = 0;
+ my $aa = $h{$t[0],$t[1]};
+ if (defined($aa)) {
+ my @aaa = split(",", $aa);
+ for (@aaa) {
+ $hit = 1 if ($_ eq $s[0]);
+ }
+ }
+ } else {
+ $hit = defined($h{$t[0],$t[1]})? 1 : 0;
+ }
+ push(@a, [$t[5], ($t[4] eq '.' || $t[4] eq $t[3])? 0 : 1, $ts{$t[3].$s[0]}? 1 : 0, $hit]);
}
push(@a, [-1, 0, 0, 0]); # end marker
die("[qstats] No SNP data!\n") if (@a == 0);
my $next = $opts{s};
my $last = $a[0];
my @c = (0, 0, 0, 0);
+ my @lc;
+ $lc[1] = $lc[2] = 0;
for my $p (@a) {
if ($p->[0] == -1 || ($p->[0] != $last && $c[0]/@a > $next)) {
my @x;
$x[0] = sprintf("%.4f", $c[1]-$c[2]? $c[2] / ($c[1] - $c[2]) : 100);
$x[1] = sprintf("%.4f", $hsize? $c[3] / $hsize : 0);
$x[2] = sprintf("%.4f", $c[3] / $c[1]);
+ my $a = $c[1] - $lc[1];
+ my $b = $c[2] - $lc[2];
+ $x[3] = sprintf("%.4f", $a-$b? $b / ($a-$b) : 100);
print join("\t", $last, @c, @x), "\n";
$next = $c[0]/@a + $opts{s};
+ $lc[1] = $c[1]; $lc[2] = $c[2];
}
++$c[0]; $c[1] += $p->[1]; $c[2] += $p->[2]; $c[3] += $p->[3];
$last = $p->[0];
}
sub varFilter {
- my %opts = (d=>1, D=>10000, l=>30, Q=>25, q=>10, G=>25, s=>100, w=>10, W=>10, N=>2, p=>undef, F=>.001);
- getopts('pq:d:D:l:Q:w:W:N:G:F:', \%opts);
+ my %opts = (d=>2, D=>10000, a=>2, W=>10, Q=>10, w=>10, p=>undef, 1=>1e-4, 2=>1e-100, 3=>0, 4=>1e-4);
+ getopts('pd:D:W:Q:w:a:1:2:3:4:', \%opts);
die(qq/
Usage: vcfutils.pl varFilter [options] <in.vcf>
Options: -Q INT minimum RMS mapping quality for SNPs [$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);
+ my $flt = 0;
+ # parse annotations
+ my ($dp, $mq, $dp_alt) = (-1, -1, -1);
if ($t[7] =~ /DP=(\d+)/i) {
$dp = $1;
} elsif ($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;
- }
- # 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 ucscsnp2vcf {
+ die("Usage: vcfutils.pl <in.ucsc.snp>\n") if (@ARGV == 0 && -t STDIN);
+ print "##fileformat=VCFv4.0\n";
+ print join("\t", "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"), "\n";
+ while (<>) {
+ my @t = split("\t");
+ my $indel = ($t[9] =~ /^[ACGT](\/[ACGT])+$/)? 0 : 1;
+ my $pos = $t[2] + 1;
+ my @alt;
+ push(@alt, $t[7]);
+ if ($t[6] eq '-') {
+ $t[9] = reverse($t[9]);
+ $t[9] =~ tr/ACGTRYMKWSNacgtrymkwsn/TGCAYRKMWSNtgcayrkmwsn/;
+ }
+ my @a = split("/", $t[9]);
+ for (@a) {
+ push(@alt, $_) if ($_ ne $alt[0]);
+ }
+ if ($indel) {
+ --$pos;
+ for (0 .. $#alt) {
+ $alt[$_] =~ tr/-//d;
+ $alt[$_] = "N$alt[$_]";
+ }
+ }
+ my $ref = shift(@alt);
+ my $af = $t[13] > 0? ";AF=$t[13]" : '';
+ my $valid = ($t[12] eq 'unknown')? '' : ";valid=$t[12]";
+ my $info = "molType=$t[10];class=$t[11]$valid$af";
+ print join("\t", $t[1], $pos, $t[4], $ref, join(",", @alt), 0, '.', $info), "\n";
}
}
qstats SNP stats stratified by QUAL
varFilter filtering short variants
hapmap2vcf convert the hapmap format to VCF
+ ucscsnp2vcf convert UCSC SNP SQL dump to VCF
\n/);
}
projects / samtools.git / blobdiff