LUYAO REN
6 years ago
1 changed files with 1 additions and 1 deletions
+ 1
- 1
tasks/Hardfiltration.wdl
View File
| command <<< | command <<< | ||||
| set -o pipefail | set -o pipefail | ||||
| set -e | 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} -window 35 -cluster 3 -filterName FS -filter "FS > 30.0" -filterName QD -filter "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" | |||||
| cat ${sample}_hc_filtered.vcf |grep "#" > ${sample}_hc_filtered.vcf.header.tmp | 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 |grep PASS > ${sample}_hc_filtered.vcf.tmp | ||||
| cat ${sample}_hc_filtered.vcf.header.tmp ${sample}_hc_filtered.vcf.tmp > ${sample}_hc_PASS.vcf | cat ${sample}_hc_filtered.vcf.header.tmp ${sample}_hc_filtered.vcf.tmp > ${sample}_hc_PASS.vcf |
Loading…