bug

codes/chemo.py

@@ -108,7 +108,14 @@ class ChemoRun:
                 record = records[(chrom, end)]
                 ref = record.ref
                 alt = record.alts[0]
-                gt = '/'.join(list(map(str, sorted(record.samples.get(record.samples.keys()[0]).get('GT')))))
+                # gt = '/'.join(list(map(str, sorted(record.samples.get(record.samples.keys()[0]).get('GT')))))
+                freq = record.samples.get(record.samples.keys()[-1]).get('AF')[0]
+                if freq > 0.9:
+                    gt = '1/1'
+                elif 0.9 >= freq > 0.1:
+                    gt = '0/1'
+                else:
+                    gt = '0/0'
                 fliter = pd.concat([fliter, drug_rsid_data[
                     (drug_rsid_data['chr'] == chrom) &
                     (drug_rsid_data['end'] == end) &

codes/filter_snpindel.pl

@@ -58,6 +58,10 @@ while (<IN>) {
     my $filters = split(";", $line[101]);
     my $gene = (split(";", $line[6]))[0];
 
+    if ($pipeline eq 'germline') {
+        $freq = (split(";", $line[-1]))[6];
+    }
+
     my @reason;
     # 黑名单
     if (exists $blacklist{join("_", @line[0 .. 4])}) {

codes/postprocess.py

@@ -241,7 +241,6 @@ 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'])