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bug

master
chaopower 2024-01-08 09:38:16 +08:00
parent e52d88516d
commit e57812a823
2 changed files with 2 additions and 1 deletions
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1
codes/postprocess.py
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@ -241,6 +241,7 @@ class PostProcess:
tmb_df = tmb_df.set_index(key_cols) 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 # 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( 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[ 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']) x, 'AMP_mut_level'] not in ['I', 'II'] else filter_sum_df.at[x, 'process'])

2
wdl/call_mutation.wdl
View File

@ -272,7 +272,7 @@ task mutation_calling_tissue_control {
vcf_filter.py -i ${output_dir}/mutation/${name}.raw.snp_indel.vcf \ vcf_filter.py -i ${output_dir}/mutation/${name}.raw.snp_indel.vcf \
-o ${output_dir}/mutation/${name}.snp_indel.germline.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'
>>> >>>