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])}) {

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'
 
     >>>