&usage if (@ARGV < 1);
my $command = shift(@ARGV);
-my %func = (showALEN=>\&showALEN, pileup2fq=>\&pileup2fq, varFilter=>\&varFilter,
+my %func = (showALEN=>\&showALEN, pileup2fq=>\&pileup2fq, varFilter=>\&varFilter, plp2vcf=>\&plp2vcf,
unique=>\&unique, uniqcmp=>\&uniqcmp, sra2hdr=>\&sra2hdr, sam2fq=>\&sam2fq);
die("Unknown command \"$command\".\n") if (!defined($func{$command}));
# G close to a high-quality indel (SNP only)
# Q low RMS mapping quality (SNP only)
# g close to another indel with higher quality (indel only)
+# s low SNP quality (SNP only)
+# i low indel quality (indel only)
sub varFilter {
- my %opts = (d=>3, D=>100, l=>30, Q=>25, q=>10, G=>25, s=>100, w=>10, W=>10, N=>2, p=>undef);
- getopts('pq:d:D:l:Q:w:W:N:G:', \%opts);
+ my %opts = (d=>3, D=>100, l=>30, Q=>25, q=>10, G=>25, s=>100, w=>10, W=>10, N=>2, p=>undef, S=>'', i=>'');
+ getopts('pq:d:D:l:Q:w:W:N:G:S:i:', \%opts);
die(qq/
Usage: samtools.pl varFilter [options] <in.cns-pileup>
-q INT minimum RMS mapping quality for gaps [$opts{q}]
-d INT minimum read depth [$opts{d}]
-D INT maximum read depth [$opts{D}]
+ -S INT minimum SNP quality [$opts{S}]
+ -i INT minimum indel quality [$opts{i}]
-G INT min indel score for nearby SNP filtering [$opts{G}]
-w INT SNP within INT bp around a gap to be filtered [$opts{w}]
next if (uc($t[2]) eq uc($t[3]) || $t[3] eq '*/*'); # skip non-var sites
# clear the out-of-range elements
while (@staging) {
- last if ($staging[0][2] eq $t[0] && $staging[0][3] + $max_dist >= $t[1]);
+ # Still on the same chromosome and the first element's window still affects this position?
+ last if ($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, $score) = (0, -1);
} elsif ($t[7] > $opts{D}) {
$flt = 3;
}
+ if ($t[2] eq '*') { # an indel
+ if ($opts{i} && $opts{i}>$t[5]) { $flt = 8; }
+ }
+ elsif ($opts{S} && $opts{S}>$t[5]) { $flt = 7; } # SNP
+
# site dependent filters
+ my $len=0;
if ($flt == 0) {
if ($t[2] eq '*') { # an indel
+ # If deletion, remember the length of the deletion
+ my ($a,$b) = split(m{/},$t[3]);
+ my $alen = length($a) - 1;
+ my $blen = length($b) - 1;
+ if ( $alen>$blen )
+ {
+ if ( substr($a,0,1) eq '-' ) { $len=$alen; }
+ }
+ elsif ( substr($b,0,1) eq '-' ) { $len=$blen; }
+
$flt = 1 if ($t[6] < $opts{q});
# filtering SNPs
if ($t[5] >= $opts{G}) {
for my $x (@staging) {
- next if ($x->[0] >= 0 || $x->[3] + $ow < $t[1]);
+ # Is it a SNP and is it outside the SNP filter window?
+ next if ($x->[0] >= 0 || $x->[4] + $x->[2] + $ow < $t[1]);
$x->[1] = 5 if ($x->[1] == 0);
}
}
$score += $opts{s} * $t[11] if ($t[9] ne '*');
# check the staging list for indel filtering
for my $x (@staging) {
- next if ($x->[0] < 0 || $x->[3] + $ol < $t[1]);
+ # Is it a SNP and is it outside the gap filter window
+ next if ($x->[0] < 0 || $x->[4] + $x->[2] + $ol < $t[1]);
if ($x->[0] < $score) {
$x->[1] = 6;
} else {
# check adjacent SNPs
my $k = 1;
for my $x (@staging) {
- ++$k if ($x->[0] < 0 && $x->[3] + $oW >= $t[1] && ($x->[1] == 0 || $x->[1] == 4 || $x->[1] == 5));
+ ++$k if ($x->[0] < 0 && $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->[3] + $oW >= $t[1] && $x->[1] == 0);
+ $x->[1] = 4 if ($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->[3] + $ow < $t[1]);
+ next if ($x->[0] < 0 || $x->[4] + $x->[2] + $ow < $t[1]);
if ($x->[0] >= $opts{G}) {
$flt = 5; last;
}
}
}
}
- push(@staging, [$score, $flt, @t]);
+ push(@staging, [$score, $flt, $len, @t]);
}
# output the last few elements in the staging list
while (@staging) {
sub varFilter_aux {
my ($first, $is_print) = @_;
if ($first->[1] == 0) {
- print join("\t", @$first[2 .. @$first-1]), "\n";
+ print join("\t", @$first[3 .. @$first-1]), "\n";
} elsif ($is_print) {
- print STDERR join("\t", substr("UQdDWGgX", $first->[1], 1), @$first[2 .. @$first-1]), "\n";
+ print STDERR join("\t", substr("UQdDWGgsiX", $first->[1], 1), @$first[3 .. @$first-1]), "\n";
}
}
close($fh);
}
+sub plp2vcf {
+ while (<>) {
+ my @t = split;
+ next if ($t[3] eq '*/*');
+ if ($t[2] eq '*') { # indel
+ my @s = split("/", $t[3]);
+ my (@a, @b);
+ my ($ref, $alt);
+ for (@s) {
+ next if ($_ eq '*');
+ if (/^-/) {
+ push(@a, 'N'.substr($_, 1));
+ push(@b, 'N');
+ } elsif (/^\+/) {
+ push(@a, 'N');
+ push(@b, 'N'.substr($_, 1));
+ }
+ }
+ if ($a[0] && $a[1]) {
+ if (length($a[0]) < length($a[1])) {
+ $ref = $a[1];
+ $alt = ($b[0] . ('N' x (length($a[1]) - length($a[0])))) . ",$b[1]";
+ } elsif (length($a[0]) > length($a[1])) {
+ $ref = $a[0];
+ $alt = ($b[1] . ('N' x (length($a[0]) - length($a[1])))) . ",$b[0]";
+ } else {
+ $ref = $a[0];
+ $alt = ($b[0] eq $b[1])? $b[0] : "$b[0],$b[1]";
+ }
+ } else {
+ $ref = $a[0]; $alt = $b[0];
+ }
+ print join("\t", @t[0,1], '.', $ref, $alt, $t[5], '.', '.'), "\n";
+ } else { # SNP
+ }
+ }
+}
+
#
# Usage
#