From 493a99cecdfe784e3d5f748e5f312d9891f3ad1e Mon Sep 17 00:00:00 2001
From: chaopower <chao.zhang@jmdna.com>
Date: Thu, 28 Dec 2023 10:41:01 +0800
Subject: [PATCH] =?UTF-8?q?=E7=BA=AF=E5=90=88=E8=B0=83=E6=95=B4=E4=B8=BA0.?=
 =?UTF-8?q?9?=
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---
 codes/hereditary.py   |  2 +-
 wdl/call_mutation.wdl | 14 +++++++-------
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/codes/hereditary.py b/codes/hereditary.py
index ab2e309..de4f6ae 100755
--- a/codes/hereditary.py
+++ b/codes/hereditary.py
@@ -45,7 +45,7 @@ class HereditaryRun:
             row_df['inheritance'] = selected_rows['inheritance']
             row_df['Gene'] = gene
             row_df['mutation'] = mutation
-            row_df['genotype'] = '纯合' if rows['Freq'] > 0.8 else '杂合'
+            row_df['genotype'] = '纯合' if rows['Freq'] > 0.9 else '杂合'
             row_df['ClinicalSign'] = str(rows['ClinicalSign'])
 
             result_df = pd.concat([result_df, row_df])
diff --git a/wdl/call_mutation.wdl b/wdl/call_mutation.wdl
index 4c477f7..4499538 100755
--- a/wdl/call_mutation.wdl
+++ b/wdl/call_mutation.wdl
@@ -27,7 +27,7 @@ task mutation_calling_umi {
         -UN -Q 20 -m 3 -r 2 -th 10 -z 1 -c 1 -S 2 -E 3 -g 4 ${bed} \
         |/dataseq/jmdna/software/VarDict-1.8.3/bin/teststrandbias.R \
         | /dataseq/jmdna/software/VarDict-1.8.3/bin/var2vcf_valid.pl \
-        -N ${name} -E -f 0.0005 > ${output_dir}/mutation/${name}.1r.vcf
+        -N ${name} -E -f 0.0005 -F 0.1 > ${output_dir}/mutation/${name}.1r.vcf
 
         #提取>=2条矫正的序列
         bam_fetch.py ${output_dir}/alignment/${name}.rmdup.bam ${output_dir}/alignment/${name}.2r.rmdup.bam
@@ -42,7 +42,7 @@ task mutation_calling_umi {
         -b ${output_dir}/alignment/${name}.2r.rmdup.bam \
         -UN -Q 20 -m 3 -r 1 -th 10 -z 1 -c 1 -S 2 -E 3 -g 4 ${bed} \
         |/dataseq/jmdna/software/VarDict-1.8.3/bin/teststrandbias.R \
-        |/dataseq/jmdna/software/VarDict-1.8.3/bin/var2vcf_valid.pl -N ${name} -E -f 0.0001 >${output_dir}/mutation/${name}.2r.vcf
+        |/dataseq/jmdna/software/VarDict-1.8.3/bin/var2vcf_valid.pl -N ${name} -E -f 0.0001 -F 0.1 >${output_dir}/mutation/${name}.2r.vcf
 
         # merge突变，以1条方式call的>0.01的突变+两条方式的对一条方式的低频区域（AF<0.01）进行矫正。
         correct_umi_1r_plus_2r.pl \
@@ -110,7 +110,7 @@ task mutation_calling_umi_control {
         -r 3 \
         -th 10 \
         -c 1 -S 2 -E 3 -g 4 ${bed} |/dataseq/jmdna/software/VarDict-1.8.3/bin/teststrandbias.R \
-        |/dataseq/jmdna/software/VarDict-1.8.3/bin/var2vcf_valid.pl -N ${name} -E -f 0.01 >${output_dir}/mutation/${name}.normal.vcf
+        |/dataseq/jmdna/software/VarDict-1.8.3/bin/var2vcf_valid.pl -N ${name} -E -f 0.01 -F 0.1 >${output_dir}/mutation/${name}.normal.vcf
 
         # 实验样本
         java -jar /dataseq/jmdna/software/VarDict-1.8.3/lib/VarDict-1.8.3.jar \
@@ -121,7 +121,7 @@ task mutation_calling_umi_control {
         -UN -Q 20 -m 3 -r 2 -th 10 -c 1 -S 2 -E 3 -g 4 ${bed} \
         | /dataseq/jmdna/software/VarDict-1.8.3/bin/teststrandbias.R \
         | /dataseq/jmdna/software/VarDict-1.8.3/bin/var2vcf_valid.pl \
-        -N ${name} -E -f 0.0005 > ${output_dir}/mutation/${name}.1r.vcf
+        -N ${name} -E -f 0.0005 -F 0.1 > ${output_dir}/mutation/${name}.1r.vcf
 
         #提取>=2条矫正的序列
         bam_fetch.py ${output_dir}/alignment/${name}.rmdup.bam ${output_dir}/alignment/${name}.2r.rmdup.bam
@@ -132,7 +132,7 @@ task mutation_calling_umi_control {
         java -jar /dataseq/jmdna/software/VarDict-1.8.3/lib/VarDict-1.8.3.jar -G ${ref} \
         -f 0.0001 -N ${name}_2r -b ${output_dir}/alignment/${name}.2r.rmdup.bam \
         -UN -Q 20 -m 3 -r 1 -th 10 -c 1 -S 2 -E 3 -g 4 ${bed} | /dataseq/jmdna/software/VarDict-1.8.3/bin/teststrandbias.R \
-        | /dataseq/jmdna/software/VarDict-1.8.3/bin/var2vcf_valid.pl -N ${name} -E -f 0.0001 >${output_dir}/mutation/${name}.2r.vcf
+        | /dataseq/jmdna/software/VarDict-1.8.3/bin/var2vcf_valid.pl -N ${name} -E -f 0.0001 -F 0.1 >${output_dir}/mutation/${name}.2r.vcf
 
         # merge突变，以1条方式call的>0.01的突变+两条方式的对一条方式的低频区域（AF<0.01）进行矫正。
         correct_umi_1r_plus_2r.pl \
@@ -203,7 +203,7 @@ task mutation_calling_tissue {
         -th 10 \
         -c 1 -S 2 -E 3 -g 4 ${bed} \
         |/dataseq/jmdna/software/VarDict-1.8.3/bin/teststrandbias.R \
-        |/dataseq/jmdna/software/VarDict-1.8.3/bin/var2vcf_valid.pl -N ${name} -E -f 0.005 \
+        |/dataseq/jmdna/software/VarDict-1.8.3/bin/var2vcf_valid.pl -N ${name} -E -f 0.005 -F 0.1 \
         >${output_dir}/mutation/${name}.raw.vcf
 
         vcf_filter.py \
@@ -255,7 +255,7 @@ task mutation_calling_tissue_control {
         -r 2 \
         -th 20 \
         -z 1 -c 1 -S 2 -E 3 -g 4 ${bed} | /dataseq/jmdna/software/VarDict-1.8.3/bin/testsomatic.R \
-        | /dataseq/jmdna/software/VarDict-1.8.3/bin/var2vcf_paired.pl -N ${name} -f 0.005 \
+        | /dataseq/jmdna/software/VarDict-1.8.3/bin/var2vcf_paired.pl -N ${name} -f 0.005 -F 0.1 \
         >${output_dir}/mutation/${name}.raw.vcf
 
         vcf_filter.py \