hardfiltration

tasks/Hardfiltration.wdl

 	command <<<
 		set -o pipefail
 		set -e
-		java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx32G -jar /gatk/gatk-package-4.1.0.0-local.jar VariantFiltration -V ${vcf_file} -O ${sample}_hc_filtered.vcf -R ${STref_dir}/${fasta} --cluster-window-size 35 --cluster-size 3 --filter-name FS --filter-expression "FS > 30.0" --filter-name QD --filter-expression "QD < 2.0"
+		java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx32G -jar /gatk/gatk-package-4.1.0.0-local.jar VariantFiltration -V ${vcf_file} -O ${sample}_hc_filtered.vcf -R ${STref_dir}/${fasta} --cluster-window-size 35 --cluster-size 3 --filter-name FS --filter-expression "FS > 30.0" --filter-name QD --filter-expression "QD < 2.0" --filter-name LowDepth --filter-expression "DP < 5"
 		cat ${sample}_hc_filtered.vcf |grep "#" > ${sample}_hc_filtered.vcf.header.tmp
 		cat ${sample}_hc_filtered.vcf |grep PASS > ${sample}_hc_filtered.vcf.tmp
 		cat ${sample}_hc_filtered.vcf.header.tmp ${sample}_hc_filtered.vcf.tmp > ${sample}_hc_PASS.vcf