From e57812a8233aadb0c8b4cc9ec91f2fbf6042768e Mon Sep 17 00:00:00 2001
From: chaopower <chao.zhang@jmdna.com>
Date: Mon, 8 Jan 2024 09:38:16 +0800
Subject: [PATCH] bug

---
 codes/postprocess.py  | 1 +
 wdl/call_mutation.wdl | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/codes/postprocess.py b/codes/postprocess.py
index 78a9a5e..1f0b5cc 100755
--- a/codes/postprocess.py
+++ b/codes/postprocess.py
@@ -241,6 +241,7 @@ class PostProcess:
             tmb_df = tmb_df.set_index(key_cols)
 
             # 在filter_sum_df中的process列中追加字符串";tmb"，对应tmb_df中的行 并且 是非 1，2类突变
+            print(tmb_df.index)
             filter_sum_df['process'] = filter_sum_df.index.map(
                 lambda x: filter_sum_df.at[x, 'process'] + ';tmb' if x in tmb_df.index and filter_sum_df.at[
                     x, 'AMP_mut_level'] not in ['I', 'II'] else filter_sum_df.at[x, 'process'])
diff --git a/wdl/call_mutation.wdl b/wdl/call_mutation.wdl
index 51ca7dd..e3bff3e 100755
--- a/wdl/call_mutation.wdl
+++ b/wdl/call_mutation.wdl
@@ -272,7 +272,7 @@ task mutation_calling_tissue_control {
 
         vcf_filter.py -i ${output_dir}/mutation/${name}.raw.snp_indel.vcf \
         -o ${output_dir}/mutation/${name}.snp_indel.germline.vcf \
-        -e 'INFO/STATUS="Germline"'
+        -e 'INFO/STATUS="Germline" && FORMAT/AF[0] > 0.1 && FORMAT/AF[1] > 0.1'
 
     >>>