1 измењених фајлова са 1 додато и 1 уклоњено
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tasks/varscan.wdl
Прегледај датотеку
| command <<< | command <<< | ||||
| samtools mpileup -f ${ref_dir}/${fasta} -B ${normal_bam} ${tumor_bam} | java -jar VarScan.v2.4.3.jar somatic --mpileup 1 --min-coverage 3 --min-coverage-normal 3 --min-coverage-tumor 3 --min-var-freq 0.08 --p-value 0.10 --somatic-p-value 0.05 --output-vcf 1 --output-snp ${sample}.VarScan.TN.SNP --output-indel ${sample}.VarScan.TN.INDEL --strand-filter 1 | |||||
| samtools mpileup -f ${ref_dir}/${fasta} -B ${normal_bam} ${tumor_bam} | java -jar /opt/VarScan.v2.4.3.jar somatic --mpileup 1 --min-coverage 3 --min-coverage-normal 3 --min-coverage-tumor 3 --min-var-freq 0.08 --p-value 0.10 --somatic-p-value 0.05 --output-vcf 1 --output-snp ${sample}.VarScan.TN.SNP --output-indel ${sample}.VarScan.TN.INDEL --strand-filter 1 | |||||
| >>> | >>> | ||||
| runtime { | runtime { |
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