merge mendelian

codescripts/linux_command.sh

@@ -3,3 +3,4 @@ cat benchmark.men.vote.diffbed.filtered | awk '{print $1"\t"$2"\t"".""\t"$35"\t"
 cat benchmark.men.vote.diffbed.filtered | awk '{print $1"\t"$2"\t"".""\t"$35"\t"$23"\t.\t.\t.\tGT\t"$22}' | grep -v '2_y' > LCL7.body
 cat benchmark.men.vote.diffbed.filtered | awk '{print $1"\t"$2"\t"".""\t"$35"\t"$31"\t.\t.\t.\tGT\t"$30}' | grep -v '2_y' > LCL8.body
 
+for i in *txt; do cat $i | awk '{ if ((length($3) == 1) && (length($4) == 1)) { print } }' | grep -v '#' | cut -f3,4 | sort |uniq -c | sed 's/\s\+/\t/g' | cut -f2 > $i.mut; done

codescripts/replicates_consensus.py

@@ -126,10 +126,24 @@ def consensus_call(vcf_info_list):
 	tag = ['inconGT','inconSequenceSite']
 	if (pcr_consensus == pcr_free_consensus) and (pcr_consensus not in tag):
 		consensus_call = pcr_consensus
+	elif (pcr_consensus in tag) and (pcr_free_consensus in tag):
+		consensus_call = 'notAgree'				
+
 	else:
 		consensus_call = 'notConsensus'
 	return consensus_call, detected_num, same_diff
 
+	elif (pcr_consensus in tag) and (pcr_free_consensus in tag):
+		consensus_call = 'filtered'				
+	elif ((pcr_consensus == './.') or (pcr_consensus in tag)) and ((pcr_free_consensus not in tag) and (pcr_free_consensus != './.')):
+		consensus_call = 'pcr-free-speicifc'				
+	elif ((pcr_consensus != './.') or (pcr_consensus not in tag)) and ((pcr_free_consensus in tag) and (pcr_free_consensus == './.')):
+		consensus_call = 'pcr-speicifc'			
+	elif (pcr_consensus == '0/0') and (pcr_free_consensus == '0/0'):
+		consensus_call = '0/0'								
+	else:
+		consensus_call = 'filtered'
+
 
 for row in vcf_dat.itertuples():
 # length