my $version = '0.1.0';
&usage if (@ARGV < 1);
my $command = shift(@ARGV);
- my %func = (subsam=>\&subsam);
+ my %func = (subsam=>\&subsam, listsam=>\&listsam, fillac=>\&fillac, qstats=>\&qstats, varFilter=>\&varFilter);
die("Unknown command \"$command\".\n") if (!defined($func{$command}));
&{$func{$command}};
}
close($fh);
}
+sub listsam {
+ die(qq/Usage: vcfutils.pl listsam <in.vcf>\n/) if (@ARGV == 0 && -t STDIN);
+ while (<>) {
+ if (/^#/ && !/^##/) {
+ my @t = split;
+ print join("\n", @t[9..$#t]), "\n";
+ exit;
+ }
+ }
+}
+
+sub fillac {
+ die(qq/Usage: vcfutils.pl fillac <in.vcf>\n\nNote: The GT field MUST BE present and always appear as the first field.\n/) if (@ARGV == 0 && -t STDIN);
+ while (<>) {
+ if (/^#/) {
+ print;
+ } else {
+ my @t = split;
+ my @c;
+ my $n = 0;
+ $c[1] = 0;
+ for (9 .. $#t) {
+ if ($t[$_] =~ /^(\d+).(\d+)/) {
+ ++$c[$1]; ++$c[$2];
+ $n += 2;
+ }
+ }
+ my $AC = "AC=" . join("\t", @c[1..$#c]) . ";AN=$n";
+ my $info = $t[7];
+ $info =~ s/(;?)AC=(\d+)//;
+ $info =~ s/(;?)AN=(\d+)//;
+ if ($info eq '.') {
+ $info = $AC;
+ } else {
+ $info .= ";$AC";
+ }
+ $t[7] = $info;
+ print join("\t", @t), "\n";
+ }
+ }
+}
+
+sub qstats {
+ my %opts = (r=>'', s=>0.01);
+ getopts('r:s:', \%opts);
+ die("Usage: vcfutils.pl qstats [-r ref.vcf] <in.vcf>\n
+Note: This command discards indels. Output: QUAL #non-indel #SNPs #transitions #joint ts/tv #joint/#ref #joint/#non-indel \n") if (@ARGV == 0 && -t STDIN);
+ my %ts = (AG=>1, GA=>1, CT=>1, TC=>1);
+ my %h = ();
+ if ($opts{r}) { # read the reference positions
+ my $fh;
+ open($fh, $opts{r}) || die;
+ while (<$fh>) {
+ next if (/^#/);
+ $h{$1,$2} = 1 if (/^(\S+)\s+(\d+)/);
+ }
+ close($fh);
+ }
+ my $hsize = scalar(keys %h);
+ my @a;
+ while (<>) {
+ next if (/^#/);
+ my @t = split;
+ next if (length($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);
+ 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],$t[1]}? 1 : 0]);
+ }
+ push(@a, [-1, 0, 0, 0]); # end marker
+ die("[qstats] No SNP data!\n") if (@a == 0);
+ @a = sort {$b->[0]<=>$a->[0]} @a;
+ my $next = $opts{s};
+ my $last = $a[0];
+ my @c = (0, 0, 0, 0);
+ for my $p (@a) {
+ if ($p->[0] == -1 || ($p->[0] != $last && $c[0]/@a > $next)) {
+ my @x;
+ $x[0] = sprintf("%.3f", $c[1]-$c[2]? $c[2] / ($c[1] - $c[2]) : 100);
+ $x[1] = sprintf("%.3f", $hsize? $c[3] / $hsize : 0);
+ $x[2] = sprintf("%.3f", $c[3] / $c[1]);
+ print join("\t", $last, @c, @x), "\n";
+ $next = $c[0]/@a + $opts{s};
+ }
+ ++$c[0]; $c[1] += $p->[1]; $c[2] += $p->[2]; $c[3] += $p->[3];
+ $last = $p->[0];
+ }
+}
+
+sub varFilter {
+ my %opts = (d=>1, D=>10000, l=>30, Q=>25, q=>10, G=>25, s=>100, w=>10, W=>10, N=>2, p=>undef, F=>.001);
+ getopts('pq:d:D:l:Q:w:W:N:G:F:', \%opts);
+ die(qq/
+Usage: vcfutils.pl varFilter [options] <in.vcf>
+
+Options: -Q INT minimum RMS mapping quality for SNPs [$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}]
+ -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}]
+
+ -p print filtered variants
+\n/) if (@ARGV == 0 && -t STDIN);
+
+ # calculate the window size
+ my ($ol, $ow, $oW) = ($opts{l}, $opts{w}, $opts{W});
+ my $max_dist = $ol > $ow? $ol : $ow;
+ $max_dist = $oW if ($max_dist < $oW);
+ # the core loop
+ my @staging; # (indel_filtering_score, flt_tag)
+ while (<>) {
+ my @t = split;
+ next if (/^#/);
+ next if ($t[4] eq '.'); # skip non-var sites
+ my $is_snp = 1;
+ if (length($t[3]) > 1) {
+ $is_snp = 0;
+ } else {
+ my @s = split(',', $t[4]);
+ for (@s) {
+ $is_snp = 0 if (length > 1);
+ }
+ }
+ # clear the out-of-range elements
+ while (@staging) {
+ # Still on the same chromosome and the first element's window still affects this position?
+ last if ($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) {
+ $dp = $1 + $2 + $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 = $1;
+ }
+ # the depth filter
+ if ($dp >= 0) {
+ if ($dp < $opts{d}) {
+ $flt = 2;
+ } elsif ($dp > $opts{D}) {
+ $flt = 3;
+ }
+ }
+
+ # site dependent filters
+ my $dlen = 0;
+ if ($flt == 0) {
+ if (!$is_snp) { # an indel
+ # If deletion, remember the length of the deletion
+ $dlen = length($t[3]) - 1;
+ $flt = 1 if ($mq < $opts{q});
+ # filtering SNPs
+ if ($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);
+ }
+ }
+ # 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) {
+ $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}) {
+ $flt = 5; last;
+ }
+ }
+ }
+ }
+ }
+ push(@staging, [$score < 0? -$af-1 : $score, $flt, $dlen, @t]);
+ }
+ # output the last few elements in the staging list
+ while (@staging) {
+ varFilter_aux(shift @staging, $opts{p});
+ }
+}
+
+sub varFilter_aux {
+ my ($first, $is_print) = @_;
+ if ($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";
+ }
+}
+
sub usage {
die(qq/
Usage: vcfutils.pl <command> [<arguments>]\n
Command: subsam get a subset of samples
+ listsam list the samples
+ fillac fill the allele count field
+ qstats SNP stats stratified by QUAL
+ varFilter filtering short variants
\n/);
}
projects / samtools.git / blobdiff