diff --git a/docm_filter.pl b/docm_filter.pl index df1066a..60e41d2 100755 --- a/docm_filter.pl +++ b/docm_filter.pl @@ -59,14 +59,18 @@ next unless $AD; my @AD = split /,/, $AD; shift @AD; #the first one is ref count - if ($set_filter_flag) { - $columns[6] = 'DOCM_ONLY'; - } + for my $ad (@AD) { if ($ad > 5 and $ad/$DP > 0.01) { my ($normal_col, $tumor_col) = map{$columns[$_]}($normal_index, $tumor_index); $columns[9] = $normal_col; $columns[10] = $tumor_col; + if ($set_filter_flag) { + $columns[6] = 'DOCM_ONLY'; + } + else { + $columns[6] = '.'; + } my $new_line = join "\t", @columns; say $docm_out_fh $new_line; last;