PASS

codescripts/merge_two_family_with_genotype.py

@@ -78,7 +78,7 @@ for row in merged_genotype_df_sub.itertuples():
 	else:
 		mendelian = mendelian + ':' + row.TRIO5.split('=')[1]
 	# family trio6
-	if row.LCL6 == row. LCL7 == row.LCL8 == './.':
+	if row.LCL6 == row.LCL7 == row.LCL8 == './.':
 		mendelian = mendelian + ':noInfo'
 	elif row.LCL6 == row. LCL7 == row.LCL8 == '0/0':
 		mendelian = mendelian + ':Ref'

tasks/benchmark.wdl

@@ -21,8 +21,14 @@ task benchmark {
 		cat unzip.vcf | grep '#CHROM' > name
 		cat unzip.vcf | grep -v '#' > body
 		cat body | grep -w '^chr1\|^chr2\|^chr3\|^chr4\|^chr5\|^chr6\|^chr7\|^chr8\|^chr9\|^chr10\|^chr11\|^chr12\|^chr13\|^chr14\|^chr15\|^chr16\|^chr17\|^chr18\|^chr19\|^chr20\|^chr21\|^chr22\|^chrX' > body.filtered
-		cat body.filtered | grep -v '0/0' > body.filtered.gt
-		cat unzip.vcf | grep '##' | grep -v 'contig' | cat - ${contig} name body.filtered.gt > filtered.vcf
+
+		if grep -q PASS "body.filtered"; then
+			cat body.filtered | grep -v '0/0' | grep 'PASS' > body.filtered.gt
+			cat unzip.vcf | grep '##' | grep -v 'contig' | cat - ${contig} name body.filtered.gt > filtered.vcf
+		else
+			cat body.filtered | grep -v '0/0' > body.filtered.gt
+			cat unzip.vcf | grep '##' | grep -v 'contig' | cat - ${contig} name body.filtered.gt > filtered.vcf
+		fi			
 
 		echo -e "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tLCL5" > LCL5_name
 		echo -e "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tLCL6" > LCL6_name