From a48795ac8b55caf9321cbe2a4199ecb3eff1fb1f Mon Sep 17 00:00:00 2001
From: chaopower <chao.zhang@jmdna.com>
Date: Thu, 28 Dec 2023 10:53:53 +0800
Subject: [PATCH] =?UTF-8?q?=E4=BF=AE=E6=94=B9=E8=A1=80=E6=B6=B2=E7=9A=84?=
 =?UTF-8?q?=E8=BF=87=E6=BB=A4=E6=9D=A1=E4=BB=B6?=
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---
 codes/filter_snpindel.pl | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

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 (<IN>) {
         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 $line[11] eq '.') {
             push @reason, 'cfdna_lowfreq_cosmic';
@@ -110,6 +110,13 @@ while (<IN>) {
             }
         }
     }
+    else {
+        # 不是pass 低频的； 或者 0.02  < 0.05 之间 个数大于2 血液 0.005 - 0.01
+        if ($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 (<IN>) {
             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'
             }