subtract -v error

campanam · Jul 17, 2022 · c944da0 · c944da0
1 parent 28f0134
commit c944da0
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/ratestools.nf b/ratestools.nf
@@ -772,7 +772,7 @@ process filterRegions {
 		#!/usr/bin/env bash
 		grep ${chr} ${exclude_bed} > tmp.bed
 		if [ ! "\$(wc -l < tmp.bed)" -eq 0 ]; then
-			zcat ${site_vcf} | bedtools subtract -a stdin -b tmp.bed -v -header | gzip > ${site_vcf.simpleName}.regionfilt.vcf.gz
+			zcat ${site_vcf} | bedtools subtract -a stdin -b tmp.bed -header | gzip > ${site_vcf.simpleName}.regionfilt.vcf.gz
 			if [[ `grep -n 'Error: Invalid record' .command.log | cut -d ':' -f 1` -eq 0 ]]; then
 				vcftools --gzvcf ${site_vcf.simpleName}.regionfilt.vcf.gz
 				cp .command.log ${site_vcf.simpleName}_regionfilt.tmp