diff --git a/codes/filter_snpindel.pl b/codes/filter_snpindel.pl index 1fad58e..837caa0 100755 --- a/codes/filter_snpindel.pl +++ b/codes/filter_snpindel.pl @@ -84,13 +84,13 @@ while () { push @reason, 'benign'; } - # 不是pass 低频的; 或者 0.02 < 0.05 之间 个数大于2 - if ($line[101] ne 'PASS' and ($freq < 0.02 or ($freq >= 0.02 and $freq < 0.05 and $filters >= 2))) { - push @reason, 'byfilter'; - } - # cfdna 样本 if ($sample_type eq 'c') { + + if ($line[101] ne 'PASS' and ($freq < 0.005 or ($freq >= 0.005 and $freq < 0.01 and $filters >= 2))) { + push @reason, 'byfilter'; + } + # 低频的 cosmic91 无记录的 if ($freq < 0.01 and $line[11] eq '.') { push @reason, 'cfdna_lowfreq_cosmic'; @@ -110,6 +110,13 @@ while () { } } } + else { + # 不是pass 低频的; 或者 0.02 < 0.05 之间 个数大于2 血液 0.005 - 0.01 + if ($line[101] ne 'PASS' and ($freq < 0.02 or ($freq >= 0.02 and $freq < 0.05 and $filters >= 2))) { + push @reason, 'byfilter'; + } + + } my $protein; if ($line[9] eq '.') { @@ -139,7 +146,7 @@ while () { else { push @reason, 'not_need_spl'; } - if ($gene eq "MET" ) { + if ($gene eq "MET") { $line[9] = join(":", ($gene, "NM_000245", "exon14", "c.xxx")); $line[8] = 'skipping' }