vcf info

tasks/variantsNorm.wdl

 
 		/opt/hall-lab/bcftools-1.9/bin/bcftools norm -f ${ref_dir}/${fasta} ${sampleName}.filtered.vcf > ${sampleName}.normed.vcf
 
+		cat ${sampleName}.normed.vcf | grep -v '#' | cut -f8 | sed s'/MQ=/\t/g' | cut -f2 | sed s'/;/\t/g' | cut -f1 > MQ
+		cat ${sampleName}.normed.vcf | grep -v '#' | awk '{print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9":MQ""\t"$10}' | paste - MQ -d ":" > body
+		cat ${sampleName}.normed.vcf | grep '#' | cat - body > ${sampleName}.normed.mq.vcf
+
 	>>>
 
 	runtime {
 	}
 	output {
 		File normed_vcf = "${sampleName}.normed.vcf"
+		File normed_mq_vcf = "${sampleName}.normed.mq.vcf"
 	}
 }

workflow.wdl

 		}
 		call zipIndex.zipIndex as LCL5normZip{
 			input:
-			vcf=LCL5variantsNorm.normed_vcf,
+			vcf=LCL5variantsNorm.normed_mq_vcf,
 			cluster_config=cluster_config,
 			disk_size=disk_size
 		}
 		call zipIndex.zipIndex as LCL6normZip{
 			input:
-			vcf=LCL6variantsNorm.normed_vcf,
+			vcf=LCL6variantsNorm.normed_mq_vcf,
 			cluster_config=cluster_config,
 			disk_size=disk_size		
 		}
 		call zipIndex.zipIndex as LCL7normZip{
 			input:
-			vcf=LCL7variantsNorm.normed_vcf,
+			vcf=LCL7variantsNorm.normed_mq_vcf,
 			cluster_config=cluster_config,
 			disk_size=disk_size		
 		}
 		call zipIndex.zipIndex as LCL8normZip{
 			input:
-			vcf=LCL8variantsNorm.normed_vcf,
+			vcf=LCL8variantsNorm.normed_mq_vcf,
 			cluster_config=cluster_config,
 			disk_size=disk_size		
 		}