From 2bc4136bb01477c1ad902409d5b090c8a4826117 Mon Sep 17 00:00:00 2001
From: chaopower <chao.zhang@jmdna.com>
Date: Tue, 9 Jan 2024 13:09:09 +0800
Subject: [PATCH] =?UTF-8?q?=E8=BF=87=E6=BB=A4=E6=9D=A1=E4=BB=B6=E8=B0=83?=
 =?UTF-8?q?=E6=95=B4?=
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---
 codes/filter_snpindel.pl | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/codes/filter_snpindel.pl b/codes/filter_snpindel.pl
index 7850d22..3405527 100755
--- a/codes/filter_snpindel.pl
+++ b/codes/filter_snpindel.pl
@@ -59,7 +59,15 @@ while (<IN>) {
     my $gene = (split(";", $line[6]))[0];
 
     if ($pipeline eq 'germline') {
-        $freq = (split(";", $line[-1]))[6];
+        # GT:DP:VD:AD:AF:RD:ALD
+        # GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM
+        # 信息提取
+        my @content_name = split(/:/, $line[103]);
+        my @content = split(/:/, $line[-1]);
+        # 将数据与表头对应
+        my %record_content;
+        @record_content{@content_name} = @content;
+        $freq = $record_content{'AF'};
     }
 
     my @reason;