X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bcftools%2Fvcfutils.pl;h=c1177eacb9603cc2cb9f93ab27d54b5add1e0779;hb=165f1d8cb88f04a48b7da3f4e5e5fd2a4f074972;hp=c625b38d774a9ae8a1ba5d213a497bc9a1f18189;hpb=d11a5b1fdadf6847f9799ee0ff0bd14b7c431cea;p=samtools.git diff --git a/bcftools/vcfutils.pl b/bcftools/vcfutils.pl index c625b38..c1177ea 100755 --- a/bcftools/vcfutils.pl +++ b/bcftools/vcfutils.pl @@ -10,11 +10,10 @@ use Getopt::Std; exit; sub main { - my $version = '0.1.0'; &usage if (@ARGV < 1); my $command = shift(@ARGV); my %func = (subsam=>\&subsam, listsam=>\&listsam, fillac=>\&fillac, qstats=>\&qstats, varFilter=>\&varFilter, - hapmap2vcf=>\&hapmap2vcf); + hapmap2vcf=>\&hapmap2vcf, ucscsnp2vcf=>\&ucscsnp2vcf, filter4vcf=>\&varFilter, ldstats=>\&ldstats); die("Unknown command \"$command\".\n") if (!defined($func{$command})); &{$func{$command}}; } @@ -70,12 +69,21 @@ 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; } } @@ -94,19 +102,47 @@ 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); } @@ -118,9 +154,22 @@ Note: This command discards indels. Output: QUAL #non-indel #SNPs #transitions # 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); @@ -128,14 +177,20 @@ 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("%.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 = $p->[0]; @@ -143,37 +198,38 @@ Note: This command discards indels. Output: QUAL #non-indel #SNPs #transitions # } sub varFilter { - my %opts = (d=>1, D=>10000, l=>30, Q=>25, q=>10, G=>25, s=>100, w=>10, W=>10, N=>2, p=>undef, F=>.001); - getopts('pq:d:D:l:Q:w:W:N:G:F:', \%opts); + my %opts = (d=>2, D=>10000, a=>2, W=>10, Q=>10, w=>10, p=>undef, 1=>1e-4, 2=>1e-100, 3=>0, 4=>1e-4); + getopts('pd:D:W:Q:w:a:1:2:3:4:', \%opts); die(qq/ Usage: vcfutils.pl varFilter [options] Options: -Q INT minimum RMS mapping quality for SNPs [$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) { $is_snp = 0; @@ -189,24 +245,17 @@ Options: -Q INT minimum RMS mapping quality for SNPs [$opts{Q}] 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}) { $flt = 2; @@ -214,58 +263,40 @@ Options: -Q INT minimum RMS mapping quality for SNPs [$opts{Q}] $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, $rlen, @t]); } # output the last few elements in the staging list while (@staging) { @@ -278,7 +309,40 @@ sub varFilter_aux { if ($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 \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"; } } @@ -343,5 +407,6 @@ Command: subsam get a subset of samples 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/); }