greo

tasks/gVCF_chromo_split.wdl

@@ -13,7 +13,7 @@ task gVCF_chromo_split {
 		cat ${gvcf} | grep '#' > header
 		for i in chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX
 		do
-			cat ${gvcf} | grep -w $i | cat header - > ${sample}.$i.vcf
+			cat ${gvcf} | grep -v '#' | grep -w $i | cat header -  > ${sample}.$i.vcf
 		done
 
 		set -o pipefail
@@ -44,6 +44,7 @@ task gVCF_chromo_split {
 		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chr22.vcf
 		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${sample}.chrX.vcf
 
+
 		>>>
 
 		runtime {