samtools command line

tasks/getBam.wdl

@@ -8,7 +8,7 @@ task getBam {
 	String disk_size
 	
 	command <<<
-			/opt/conda/bin/samtools view ${bam} -H ${sep=" " pos} | /opt/conda/bin/samtools view -bS - | /opt/conda/bin/samtools sort > ${sample}.bam
+			/opt/conda/bin/samtools view -b ${bam} ${sep=" " pos} | opt/conda/bin/samtools sort - > ${sample}.bam
 			/opt/conda/bin/samtools index ${sample}.bam
 	>>>