X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fvcfutils.pl;h=bbc479bfffa47aa2b1089b5b6e56414b696be413;hb=95b7e2d5d54f2b10bef8dd937e43c342d2086b46;hp=0fe1af88014c8b94e9b761e96f2da57be3be545e;hpb=7ef82722e41143d313b37394b905239ae61ca19a;p=samtools.git diff --git a/bcftools/vcfutils.pl b/bcftools/vcfutils.pl index 0fe1af8..bbc479b 100755 --- a/bcftools/vcfutils.pl +++ b/bcftools/vcfutils.pl @@ -10,10 +10,11 @@ use Getopt::Std; exit; sub main { - my $version = '0.1.0'; &usage if (@ARGV < 1); my $command = shift(@ARGV); - my %func = (subsam=>\&subsam, listsam=>\&listsam, fillac=>\&fillac, qstats=>\&qstats); + my %func = (subsam=>\&subsam, listsam=>\&listsam, fillac=>\&fillac, qstats=>\&qstats, varFilter=>\&varFilter, + hapmap2vcf=>\&hapmap2vcf, ucscsnp2vcf=>\&ucscsnp2vcf, filter4vcf=>\&varFilter, ldstats=>\&ldstats, + gapstats=>\&gapstats); die("Unknown command \"$command\".\n") if (!defined($func{$command})); &{$func{$command}}; } @@ -69,12 +70,21 @@ sub fillac { 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; } } @@ -93,19 +103,47 @@ sub fillac { } } +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=>0.01); - 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] \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); } @@ -115,10 +153,24 @@ Note: This command discards indels. Output: QUAL #non-indel #SNPs #transitions # next if (/^#/); my @t = split; next if (length($t[3]) != 1 || uc($t[3]) eq 'N'); - my @s = split(',', $t[4]); $t[3] = uc($t[3]); $t[4] = uc($t[4]); + my @s = split(',', $t[4]); + $t[5] = 3 if ($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); @@ -126,20 +178,255 @@ Note: This command discards indels. Output: QUAL #non-indel #SNPs #transitions # 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("%.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[0]); + $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 = $p->[0]; } } +sub varFilter { + my %opts = (d=>2, D=>10000, a=>2, W=>10, Q=>10, w=>10, p=>undef, 1=>1e-4, 2=>1e-100, 3=>0, 4=>1e-4); + getopts('pd:D:W:Q:w:a:1:2:3:4:', \%opts); + die(qq/ +Usage: vcfutils.pl varFilter [options] + +Options: -Q INT minimum RMS mapping quality for SNPs [$opts{Q}] + -d INT minimum read depth [$opts{d}] + -D INT maximum read depth [$opts{D}] + -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 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, $ow) = ($opts{W}, $opts{w}); + my $max_dist = $ol > $ow? $ol : $ow; + # the core loop + my @staging; # (indel_filtering_score, flt_tag, indel_span; chr, pos, ...) + while (<>) { + my @t = split; + if (/^#/) { + print; next; + } + next if ($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; + } 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 $flt = 0; + # parse annotations + my ($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] =~ /DP=(\d+)/i) { + $dp = $1; + } + $mq = $1 if ($t[7] =~ /MQ=(\d+)/i); + # the depth and mapQ filter + if ($dp >= 0) { + if ($dp < $opts{d}) { + $flt = 2; + } elsif ($dp > $opts{D}) { + $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 ($rlen, $indel_score) = (0, -1); # $indel_score<0 for SNPs + if ($flt == 0) { + if (!$is_snp) { # an indel + $rlen = length($t[3]) - 1; + $indel_score = $t[5] * 100 + $dp_alt; + # filtering SNPs + for my $x (@staging) { + next if ($x->[0] >= 0 || $x->[1] || $x->[4] + $x->[2] + $ow < $t[1]); + $x->[1] = 5; + } + # check the staging list for indel filtering + for my $x (@staging) { + next if ($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 + for my $x (@staging) { + next if ($x->[0] < 0 || $x->[1] || $x->[4] + $x->[2] + $ow < $t[1]); + $flt = 5; + last; + } + } + } + push(@staging, [$indel_score, $flt, $rlen, @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("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 { + 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 @@ -147,5 +434,8 @@ 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 + hapmap2vcf convert the hapmap format to VCF + ucscsnp2vcf convert UCSC SNP SQL dump to VCF \n/); }