diff --git a/script/filter_snpindel.pl b/script/filter_snpindel.pl index 57efe45..7fd3ef3 100755 --- a/script/filter_snpindel.pl +++ b/script/filter_snpindel.pl @@ -123,8 +123,16 @@ while () { } $hgvs =~ /(\S+):exon(\d+):c\.(\S+)$/; my $spl = $3; + my $exon = $2; # splicing 位点 的前后 1-2bp 的 或者 MET的基因 - if ($spl =~ /\d+[\+|\-][1|2]\D+/) { + if ($spl =~ /\d+\+[1|2]\D+/) { + my $intron = $exon; + $hgvs =~ s/exon(\d+)/exon$exon;intron$intron/; + $line[9] = join(":", ($gene, $hgvs)); + } + elsif ($spl =~ /\d+\-[1|2]\D+/) { + my $intron = $exon-1; + $hgvs =~ s/exon(\d+)/intron$intron;exon$exon/; $line[9] = join(":", ($gene, $hgvs)); } elsif ($gene eq "MET") {