column name

codescripts/filter_indel_over_50.py

 		alt_len = [len(i) for i in alt]
 		alt_max = max(alt_len)
 	else:
-		alt_max = len(strings[6])
+		alt_max = len(strings[3])
 #ref
-	ref_len = len(strings[34])
+	ref_len = len(strings[2])
 	if (alt_max > 50) or (ref_len > 50):
 		pass
 	else:

tasks/Jaccard_Index.wdl

 	cat ${chromo}.gt | awk '{ if ((length($3) == 1) && (length($4) == 1)) { print } }' > ${chromo}.gt.snv
 	cat ${chromo}.gt | awk '{ if ((length($3) != 1) || (length($4) != 1)) { print } }' > ${chromo}.gt.indel
 
-	python /opt/library_concordance.py -i ${chromo}.gt.snv -prefix ${chromo}.snv
+	cat ${chromo}.gt | head -n1 | cat - ${chromo}.gt.snv > ${chromo}.gt.snv.txt
+	python /opt/library_concordance.py -i ${chromo}.gt.snv.txt -prefix ${chromo}.snv
 	python /opt/filter_indel_over_50.py -i ${chromo}.gt.indel -prefix ${chromo}
-	python /opt/library_concordance.py -i ${chromo}.indel.lessthan50bp.txt -prefix ${chromo}.indel
+	cat ${chromo}.gt | head -n1 | cat - ${chromo}.indel.lessthan50bp.txt > ${chromo}.gt.indel.txt
+	python /opt/library_concordance.py -i ${chromo}.gt.indel.txt -prefix ${chromo}.indel
 
 	>>>
 
 	}
 	output {
 		File genotype = "${chromo}.gt"
-		File snv = "${chromo}.gt.snv"
-		File indel = "${chromo}.indel.lessthan50bp.txt"
+		File snv = "${chromo}.gt.snv.txt"
+		File indel = "${chromo}.indel.txt"
 		File snv_inter = "${chromo}.snv.inter.txt"
 		File snv_union = "${chromo}.snv.union.txt"
 		File indel_inter = "${chromo}.indel.inter.txt"