13 &usage if (@ARGV < 1);
14 my $command = shift(@ARGV);
15 my %func = (subsam=>\&subsam, listsam=>\&listsam, fillac=>\&fillac, qstats=>\&qstats, varFilter=>\&varFilter,
16 hapmap2vcf=>\&hapmap2vcf, ucscsnp2vcf=>\&ucscsnp2vcf, filter4vcf=>\&varFilter, ldstats=>\&ldstats,
17 gapstats=>\&gapstats, splitchr=>\&splitchr, vcf2fq=>\&vcf2fq);
18 die("Unknown command \"$command\".\n") if (!defined($func{$command}));
23 my %opts = (l=>5000000);
24 getopts('l:', \%opts);
26 die(qq/Usage: vcfutils.pl splitchr [-l $opts{l}] <in.fa.fai>\n/) if (@ARGV == 0 && -t STDIN);
30 for (my $i = 0; $i < $t[1];) {
31 my $e = ($t[1] - $i) / $l < 1.1? $t[1] : $i + $l;
32 print "$t[0]:".($i+1)."-$e\n";
39 die(qq/Usage: vcfutils.pl subsam <in.vcf> [samples]\n/) if (@ARGV == 0);
41 my $fn = shift(@ARGV);
43 open($fh, ($fn =~ /\.gz$/)? "gzip -dc $fn |" : $fn) || die;
44 $h{$_} = 1 for (@ARGV);
50 my @s = @t[0..8]; # all fixed fields + FORMAT
57 pop(@s) if (@s == 9); # no sample selected; remove the FORMAT field
58 print join("\t", @s), "\n";
62 print join("\t", @t[0..7]), "\n";
64 print join("\t", @t[0..8], map {$t[$_]} @col), "\n";
72 die(qq/Usage: vcfutils.pl listsam <in.vcf>\n/) if (@ARGV == 0 && -t STDIN);
76 print join("\n", @t[9..$#t]), "\n";
83 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);
92 @_ = split(":", $t[8]);
94 if ($_[$_] eq 'GT') { $s = $_; last; }
97 print join("\t", @t), "\n";
101 if ($t[$_] =~ /^0,0,0/) {
102 } elsif ($t[$_] =~ /^([^\s:]+:){$s}(\d+).(\d+)/) {
107 my $AC = "AC=" . join("\t", @c[1..$#c]) . ";AN=$n";
109 $info =~ s/(;?)AC=(\d+)//;
110 $info =~ s/(;?)AN=(\d+)//;
117 print join("\t", @t), "\n";
124 getopts('t:', \%opts);
125 die("Usage: vcfutils.pl ldstats [-t $opts{t}] <in.vcf>\n") if (@ARGV == 0 && -t STDIN);
126 my $cutoff = $opts{t};
127 my ($last, $lastchr) = (0x7fffffff, '');
128 my ($x, $y, $n) = (0, 0, 0);
130 if (/^([^#\s]+)\s(\d+)/) {
131 my ($chr, $pos) = ($1, $2);
132 if (/NEIR=([\d\.]+)/) {
134 ++$y, $x += $pos - $last if ($lastchr eq $chr && $pos > $last && $1 > $cutoff);
136 $last = $pos; $lastchr = $chr;
139 print "Number of SNP intervals in strong LD (r > $opts{t}): $y\n";
140 print "Fraction: ", $y/$n, "\n";
141 print "Length: $x\n";
145 my %opts = (r=>'', s=>0.02, v=>undef);
146 getopts('r:s:v', \%opts);
147 die("Usage: vcfutils.pl qstats [-r ref.vcf] <in.vcf>\n
148 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);
149 my %ts = (AG=>1, GA=>1, CT=>1, TC=>1);
151 my $is_vcf = defined($opts{v})? 1 : 0;
152 if ($opts{r}) { # read the reference positions
154 open($fh, $opts{r}) || die;
159 $h{$t[0],$t[1]} = $t[4];
161 $h{$1,$2} = 1 if (/^(\S+)\s+(\d+)/);
166 my $hsize = scalar(keys %h);
171 next if (length($t[3]) != 1 || uc($t[3]) eq 'N');
172 $t[3] = uc($t[3]); $t[4] = uc($t[4]);
173 my @s = split(',', $t[4]);
174 $t[5] = 3 if ($t[5] eq '.' || $t[5] < 0);
175 next if (length($s[0]) != 1);
179 my $aa = $h{$t[0],$t[1]};
181 my @aaa = split(",", $aa);
183 $hit = 1 if ($_ eq $s[0]);
187 $hit = defined($h{$t[0],$t[1]})? 1 : 0;
189 push(@a, [$t[5], ($t[4] eq '.' || $t[4] eq $t[3])? 0 : 1, $ts{$t[3].$s[0]}? 1 : 0, $hit]);
191 push(@a, [-1, 0, 0, 0]); # end marker
192 die("[qstats] No SNP data!\n") if (@a == 0);
193 @a = sort {$b->[0]<=>$a->[0]} @a;
196 my @c = (0, 0, 0, 0);
200 if ($p->[0] == -1 || ($p->[0] != $last && $c[0]/@a > $next)) {
202 $x[0] = sprintf("%.4f", $c[1]-$c[2]? $c[2] / ($c[1] - $c[2]) : 100);
203 $x[1] = sprintf("%.4f", $hsize? $c[3] / $hsize : 0);
204 $x[2] = sprintf("%.4f", $c[3] / $c[1]);
205 my $a = $c[1] - $lc[1];
206 my $b = $c[2] - $lc[2];
207 $x[3] = sprintf("%.4f", $a-$b? $b / ($a-$b) : 100);
208 print join("\t", $last, @c, @x), "\n";
209 $next = $c[0]/@a + $opts{s};
210 $lc[1] = $c[1]; $lc[2] = $c[2];
212 ++$c[0]; $c[1] += $p->[1]; $c[2] += $p->[2]; $c[3] += $p->[3];
218 my %opts = (d=>2, D=>10000000, a=>2, W=>10, Q=>10, w=>3, p=>undef, 1=>1e-4, 2=>1e-100, 3=>0, 4=>1e-4, G=>0, S=>1000, e=>1e-4);
219 getopts('pd:D:W:Q:w:a:1:2:3:4:G:S:e:', \%opts);
221 Usage: vcfutils.pl varFilter [options] <in.vcf>
223 Options: -Q INT minimum RMS mapping quality for SNPs [$opts{Q}]
224 -d INT minimum read depth [$opts{d}]
225 -D INT maximum read depth [$opts{D}]
226 -a INT minimum number of alternate bases [$opts{a}]
227 -w INT SNP within INT bp around a gap to be filtered [$opts{w}]
228 -W INT window size for filtering adjacent gaps [$opts{W}]
229 -1 FLOAT min P-value for strand bias (given PV4) [$opts{1}]
230 -2 FLOAT min P-value for baseQ bias [$opts{2}]
231 -3 FLOAT min P-value for mapQ bias [$opts{3}]
232 -4 FLOAT min P-value for end distance bias [$opts{4}]
233 -e FLOAT min P-value for HWE (plus F<0) [$opts{e}]
234 -p print filtered variants
236 Note: Some of the filters rely on annotations generated by SAMtools\/BCFtools.
237 \n/) if (@ARGV == 0 && -t STDIN);
239 # calculate the window size
240 my ($ol, $ow) = ($opts{W}, $opts{w});
241 my $max_dist = $ol > $ow? $ol : $ow;
243 my @staging; # (indel_filtering_score, flt_tag, indel_span; chr, pos, ...)
249 next if ($t[4] eq '.'); # skip non-var sites
250 next if ($t[3] eq 'N'); # skip sites with unknown ref ('N')
251 # check if the site is a SNP
253 if (length($t[3]) > 1) {
255 my @s = split(',', $t[4]);
257 $type = 3 if (length != length($t[3]));
260 my @s = split(',', $t[4]);
262 $type = 3 if (length > 1);
265 # clear the out-of-range elements
267 # Still on the same chromosome and the first element's window still affects this position?
268 last if ($staging[0][3] eq $t[0] && $staging[0][4] + $staging[0][2] + $max_dist >= $t[1]);
269 varFilter_aux(shift(@staging), $opts{p}); # calling a function is a bit slower, not much
273 my ($dp, $mq, $dp_alt) = (-1, -1, -1);
274 if ($t[7] =~ /DP4=(\d+),(\d+),(\d+),(\d+)/i) {
275 $dp = $1 + $2 + $3 + $4;
278 if ($t[7] =~ /DP=(\d+)/i) {
281 $mq = $1 if ($t[7] =~ /MQ=(\d+)/i);
282 # the depth and mapQ filter
284 if ($dp < $opts{d}) {
286 } elsif ($dp > $opts{D}) {
290 $flt = 4 if ($dp_alt >= 0 && $dp_alt < $opts{a});
291 $flt = 1 if ($flt == 0 && $mq >= 0 && $mq < $opts{Q});
292 $flt = 7 if ($flt == 0 && /PV4=([^,]+),([^,]+),([^,]+),([^,;\t]+)/
293 && ($1<$opts{1} || $2<$opts{2} || $3<$opts{3} || $4<$opts{4}));
294 $flt = 8 if ($flt == 0 && ((/MXGQ=(\d+)/ && $1 < $opts{G}) || (/MXSP=(\d+)/ && $1 >= $opts{S})));
296 if ($t[7] =~ /G3=([^;,]+),([^;,]+),([^;,]+).*HWE=([^;,]+)/ && $4 < $opts{e}) {
298 my $f = ($p > 0 && $p < 1)? 1 - $2 / ($p * (1-$p)) : 0;
299 $flt = 9 if ($f < 0);
302 my $score = $t[5] * 100 + $dp_alt;
303 my $rlen = length($t[3]) - 1; # $indel_score<0 for SNPs
305 if ($type == 3) { # an indel
306 # filtering SNPs and MNPs
307 for my $x (@staging) {
308 next if (($x->[0]&3) == 3 || $x->[1] || $x->[4] + $x->[2] + $ow < $t[1]);
311 # check the staging list for indel filtering
312 for my $x (@staging) {
313 next if (($x->[0]&3) != 3 || $x->[1] || $x->[4] + $x->[2] + $ol < $t[1]);
314 if ($x->[0]>>2 < $score) {
320 } else { # SNP or MNP
321 for my $x (@staging) {
322 next if (($x->[0]&3) != 3 || $x->[4] + $x->[2] + $ow < $t[1]);
323 if ($x->[4] + length($x->[7]) - 1 == $t[1] && substr($x->[7], -1, 1) eq substr($t[4], 0, 1)
324 && length($x->[7]) - length($x->[6]) == 1) {
330 for my $x (@staging) {
331 next if (($x->[0]&3) == 3 || $x->[4] + $x->[2] < $t[1]);
332 if ($x->[0]>>2 < $score) {
340 push(@staging, [$score<<2|$type, $flt, $rlen, @t]);
342 # output the last few elements in the staging list
344 varFilter_aux(shift @staging, $opts{p});
349 my ($first, $is_print) = @_;
350 if ($first->[1] == 0) {
351 print join("\t", @$first[3 .. @$first-1]), "\n";
352 } elsif ($is_print) {
353 print STDERR join("\t", substr("UQdDaGgPMS", $first->[1], 1), @$first[3 .. @$first-1]), "\n";
359 $c0[$_] = $c1[$_] = 0 for (0 .. 10000);
363 next if (length($t[3]) == 1 && $t[4] =~ /^[A-Za-z](,[A-Za-z])*$/); # not an indel
364 my @s = split(',', $t[4]);
366 my $l = length($x) - length($t[3]) + 5000;
368 $l = -(length($x) - 1) + 5000;
369 } elsif ($x =~ /^\+/) {
370 $l = length($x) - 1 + 5000;
375 for (my $i = 0; $i < 10000; ++$i) {
376 next if ($c0[$i] == 0);
378 $c1[1] += $c0[$i] if (($i-5000)%3 == 0);
379 printf("C\t%d\t%.2f\n", ($i-5000), $c0[$i]);
381 printf("3\t%d\t%d\t%.3f\n", $c1[0], $c1[1], $c1[1]/$c1[0]);
385 die("Usage: vcfutils.pl <in.ucsc.snp>\n") if (@ARGV == 0 && -t STDIN);
386 print "##fileformat=VCFv4.0\n";
387 print join("\t", "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"), "\n";
390 my $indel = ($t[9] =~ /^[ACGT](\/[ACGT])+$/)? 0 : 1;
395 $t[9] = reverse($t[9]);
396 $t[9] =~ tr/ACGTRYMKWSNacgtrymkwsn/TGCAYRKMWSNtgcayrkmwsn/;
398 my @a = split("/", $t[9]);
400 push(@alt, $_) if ($_ ne $alt[0]);
406 $alt[$_] = "N$alt[$_]";
409 my $ref = shift(@alt);
410 my $af = $t[13] > 0? ";AF=$t[13]" : '';
411 my $valid = ($t[12] eq 'unknown')? '' : ";valid=$t[12]";
412 my $info = "molType=$t[10];class=$t[11]$valid$af";
413 print join("\t", $t[1], $pos, $t[4], $ref, join(",", @alt), 0, '.', $info), "\n";
418 die("Usage: vcfutils.pl <in.ucsc.snp> <in.hapmap>\n") if (@ARGV == 0);
419 my $fn = shift(@ARGV);
421 warn("Parsing UCSC SNPs...\n");
423 open($fh, ($fn =~ /\.gz$/)? "gzip -dc $fn |" : $fn) || die;
426 next if ($t[3] - $t[2] != 1); # not SNP
427 @{$map{$t[4]}} = @t[1,3,7];
431 warn("Writing VCF...\n");
432 print "##fileformat=VCFv4.0\n";
435 if ($t[0] eq 'rs#') { # the first line
436 print join("\t", "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT", @t[11..$#t]), "\n";
438 next unless ($map{$t[0]});
439 next if (length($t[1]) != 3); # skip non-SNPs
440 my $a = \@{$map{$t[0]}};
442 my @u = split('/', $t[1]);
444 $u[1] = $u[0]; $u[0] = $ref;
445 } elsif ($u[0] ne $ref) { next; }
448 $w{$u[0]} = 0; $w{$u[1]} = 1;
449 my @s = (@$a[0,1], $t[0], $ref, $alt, 0, '.', '.', 'GT');
455 my @a = ($w{substr($_,0,1)}, $w{substr($_,1,1)});
456 if (!defined($a[0]) || !defined($a[1])) {
460 push(@s, "$a[0]/$a[1]");
464 print join("\t", @s), "\n";
470 my %opts = (d=>3, D=>100000, Q=>10, l=>5);
471 getopts('d:D:Q:l:', \%opts);
473 Usage: vcfutils.pl vcf2fq [options] <all-site.vcf>
475 Options: -d INT minimum depth [$opts{d}]
476 -D INT maximum depth [$opts{D}]
477 -Q INT min RMS mapQ [$opts{Q}]
478 -l INT INDEL filtering window [$opts{l}]
479 \n/) if (@ARGV == 0 && -t STDIN);
481 my ($last_chr, $seq, $qual, $last_pos, @gaps);
486 my %het = (AC=>'M', AG=>'R', AT=>'W', CA=>'M', CG=>'S', CT=>'Y',
487 GA=>'R', GC=>'S', GT=>'K', TA=>'W', TC=>'Y', TG=>'K');
493 if ($last_chr ne $t[0]) {
494 &v2q_post_process($last_chr, \$seq, \$qual, \@gaps, $opts{l}) if ($last_chr);
495 ($last_chr, $last_pos) = ($t[0], 0);
499 die("[vcf2fq] unsorted input\n") if ($t[1] - $last_pos < 0);
500 if ($t[1] - $last_pos > 1) {
501 $seq .= 'n' x ($t[1] - $last_pos - 1);
502 $qual .= '!' x ($t[1] - $last_pos - 1);
504 if (length($t[3]) == 1 && $t[7] !~ /INDEL/ && $t[4] =~ /^([A-Za-z.])(,[A-Za-z])*$/) { # a SNP or reference
505 my ($ref, $alt) = ($t[3], $1);
507 $q = $1 if ($t[7] =~ /FQ=(-?[\d\.]+)/);
509 $_ = ($t[7] =~ /AF1=([\d\.]+)/)? $1 : 0;
510 $b = ($_ < .5 || $alt eq '.')? $ref : $alt;
513 $b = $het{"$ref$alt"};
517 $b = uc($b) if (($t[7] =~ /MQ=(\d+)/ && $1 >= $_Q) && ($t[7] =~ /DP=(\d+)/ && $1 >= $_d && $1 <= $_D));
518 $q = int($q + 33 + .499);
519 $q = chr($q <= 126? $q : 126);
522 } elsif ($t[4] ne '.') { # an INDEL
523 push(@gaps, [$t[1], length($t[3])]);
527 &v2q_post_process($last_chr, \$seq, \$qual, \@gaps, $opts{l});
530 sub v2q_post_process {
531 my ($chr, $seq, $qual, $gaps, $l) = @_;
533 my $beg = $g->[0] > $l? $g->[0] - $l : 0;
534 my $end = $g->[0] + $g->[1] + $l;
535 $end = length($$seq) if ($end > length($$seq));
536 substr($$seq, $beg, $end - $beg) = lc(substr($$seq, $beg, $end - $beg));
538 print "\@$chr\n"; &v2q_print_str($seq);
539 print "+\n"; &v2q_print_str($qual);
545 for (my $i = 0; $i < $l; $i += 60) {
546 print substr($$s, $i, 60), "\n";
552 Usage: vcfutils.pl <command> [<arguments>]\n
553 Command: subsam get a subset of samples
554 listsam list the samples
555 fillac fill the allele count field
556 qstats SNP stats stratified by QUAL
558 hapmap2vcf convert the hapmap format to VCF
559 ucscsnp2vcf convert UCSC SNP SQL dump to VCF
561 varFilter filtering short variants (*)
562 vcf2fq VCF->fastq (**)
564 Notes: Commands with description endting with (*) may need bcftools
565 specific annotations.