X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bcftools%2Fvcfutils.pl;fp=bcftools%2Fvcfutils.pl;h=d0b797143cf56fe0a67383ec4f610096eaecf2c0;hp=0000000000000000000000000000000000000000;hb=8d2494d1fb7cd0fa7c63be5ffba8dd1a11457522;hpb=cb12a866906ec4ac644de0e658679261c82ab098 diff --git a/bcftools/vcfutils.pl b/bcftools/vcfutils.pl new file mode 100755 index 0000000..d0b7971 --- /dev/null +++ b/bcftools/vcfutils.pl @@ -0,0 +1,477 @@ +#!/usr/bin/perl -w + +# Author: lh3 + +use strict; +use warnings; +use Getopt::Std; + +&main; +exit; + +sub main { + my $version = '0.1.0'; + &usage if (@ARGV < 1); + my $command = shift(@ARGV); + my %func = (subsam=>\&subsam, listsam=>\&listsam, fillac=>\&fillac, qstats=>\&qstats, varFilter=>\&varFilter, + hapmap2vcf=>\&hapmap2vcf, ucscsnp2vcf=>\&ucscsnp2vcf, filter4vcf=>\&filter4vcf, ldstats=>\&ldstats); + die("Unknown command \"$command\".\n") if (!defined($func{$command})); + &{$func{$command}}; +} + +sub subsam { + die(qq/Usage: vcfutils.pl subsam [samples]\n/) if (@ARGV == 0); + my ($fh, %h); + my $fn = shift(@ARGV); + my @col; + open($fh, ($fn =~ /\.gz$/)? "gzip -dc $fn |" : $fn) || die; + $h{$_} = 1 for (@ARGV); + while (<$fh>) { + if (/^##/) { + print; + } elsif (/^#/) { + my @t = split; + my @s = @t[0..8]; # all fixed fields + FORMAT + for (9 .. $#t) { + if ($h{$t[$_]}) { + push(@s, $t[$_]); + push(@col, $_); + } + } + pop(@s) if (@s == 9); # no sample selected; remove the FORMAT field + print join("\t", @s), "\n"; + } else { + my @t = split; + if (@col == 0) { + print join("\t", @t[0..7]), "\n"; + } else { + print join("\t", @t[0..8], map {$t[$_]} @col), "\n"; + } + } + } + close($fh); +} + +sub listsam { + die(qq/Usage: vcfutils.pl listsam \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 \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 = (0); + my $n = 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[$_] =~ /^0,0,0/) { + } elsif ($t[$_] =~ /^([^\s:]+:){$s}(\d+).(\d+)/) { + ++$c[$2]; ++$c[$3]; + $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 ldstats { + my %opts = (t=>0.9); + getopts('t:', \%opts); + die("Usage: vcfutils.pl ldstats [-t $opts{t}] \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); + die("Usage: vcfutils.pl qstats [-r ref.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 (/^#/); + if ($is_vcf) { + my @t = split; + $h{$t[0],$t[1]} = $t[4]; + } else { + $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); + 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, $hit]); + } + push(@a, [-1, 0, 0, 0]); # end marker + die("[qstats] No SNP data!\n") if (@a == 0); + @a = sort {$b->[0]<=>$a->[0]} @a; + 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 = $p->[0]; + } +} + +sub varFilter { + my %opts = (d=>1, D=>10000, l=>30, Q=>25, q=>10, G=>25, s=>100, w=>10, W=>10, N=>2, p=>undef, F=>.001); + getopts('pq:d:D:l:Q:w:W:N:G:F:', \%opts); + die(qq/ +Usage: vcfutils.pl varFilter [options] + +Options: -Q INT minimum RMS mapping quality for SNPs [$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 .. @$first-1]), "\n"; + } +} + +sub filter4vcf { + my %opts = (d=>3, D=>2000, 1=>1e-4, 2=>1e-100, 3=>0, 4=>1e-4, Q=>10, q=>3); + getopts('d:D:1:2:3:4:Q:q:', \%opts); + die(qq/ +Usage: vcfutils.pl filter4vcf [options] + +Options: -d INT min total depth (given DP or DP4) [$opts{d}] + -D INT max total depth [$opts{D}] + -q INT min SNP quality [$opts{q}] + -Q INT min RMS mapQ (given MQ) [$opts{Q}] + -1 FLOAT min P-value for strand bias (given PV4) [$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}]\n +/) if (@ARGV == 0 && -t STDIN); + + my %ts = (AG=>1, GA=>1, CT=>1, TC=>1); + + my @n = (0, 0); + while (<>) { + if (/^#/) { + print; + next; + } + next if (/PV4=([^,]+),([^,]+),([^,]+),([^,;\t]+)/ && ($1<$opts{1} || $2<$opts{2} || $3<$opts{3} || $4<$opts{4})); + my $depth = -1; + $depth = $1 if (/DP=(\d+)/); + $depth = $1+$2+$3+$4 if (/DP4=(\d+),(\d+),(\d+),(\d+)/); + next if ($depth > 0 && ($depth < $opts{d} || $depth > $opts{D})); + next if (/MQ=(\d+)/ && $1 < $opts{Q}); + my @t = split; + next if ($t[5] >= 0 && $t[5] < $opts{q}); + ++$n[0]; + my @s = split(',', $t[4]); + ++$n[1] if ($ts{$t[3].$s[0]}); + print; + } +} + +sub ucscsnp2vcf { + die("Usage: vcfutils.pl \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"; + } +} + +sub hapmap2vcf { + die("Usage: vcfutils.pl \n") if (@ARGV == 0); + my $fn = shift(@ARGV); + # parse UCSC SNP + warn("Parsing UCSC SNPs...\n"); + my ($fh, %map); + open($fh, ($fn =~ /\.gz$/)? "gzip -dc $fn |" : $fn) || die; + while (<$fh>) { + my @t = split; + next if ($t[3] - $t[2] != 1); # not SNP + @{$map{$t[4]}} = @t[1,3,7]; + } + close($fh); + # write VCF + warn("Writing VCF...\n"); + print "##fileformat=VCFv4.0\n"; + while (<>) { + my @t = split; + if ($t[0] eq 'rs#') { # the first line + print join("\t", "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT", @t[11..$#t]), "\n"; + } else { + next unless ($map{$t[0]}); + next if (length($t[1]) != 3); # skip non-SNPs + my $a = \@{$map{$t[0]}}; + my $ref = $a->[2]; + my @u = split('/', $t[1]); + if ($u[1] eq $ref) { + $u[1] = $u[0]; $u[0] = $ref; + } elsif ($u[0] ne $ref) { next; } + my $alt = $u[1]; + my %w; + $w{$u[0]} = 0; $w{$u[1]} = 1; + my @s = (@$a[0,1], $t[0], $ref, $alt, 0, '.', '.', 'GT'); + my $is_tri = 0; + for (@t[11..$#t]) { + if ($_ eq 'NN') { + push(@s, './.'); + } else { + my @a = ($w{substr($_,0,1)}, $w{substr($_,1,1)}); + if (!defined($a[0]) || !defined($a[1])) { + $is_tri = 1; + last; + } + push(@s, "$a[0]/$a[1]"); + } + } + next if ($is_tri); + print join("\t", @s), "\n"; + } + } +} + +sub usage { + die(qq/ +Usage: vcfutils.pl []\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 + filter4vcf filtering VCFs produced by samtools+bcftools + hapmap2vcf convert the hapmap format to VCF + ucscsnp2vcf convert UCSC SNP SQL dump to VCF +\n/); +}