.command.out - Workdir - NFCORE_RNAFUSION:RNAFUSION:RNA_CONTAMINATION_DETECTION_WORKFLOW:NGSCheckMATE (HD789_0002_RNA_0008_23H5VFLT4_s19)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/4c9e8dfce5f75e419004ae1466d130/.command.out
Size: 461 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:RNA_CONTAMINATION_DETECTION_WORKFLOW:NGSCheckMATE (HD789_0002_RNA_0008_23H5VFLT4_s19)
Attempt

Content

Set the path to your reference file with the NCM_REF environment variable
eg. export NCM_REF=/<path>/<to>/<reference>

1.14
samtools mpileup -uf $NCM_REF -l /usr/local/NGSCheckMate/SNP/SNP_GRCh38_hg38_wChr.bed HD789_0002_RNA_0008_23H5VFLT4_s19.Aligned.sortedByCoord.out.bam | bcftools call -c > ./HD789_0002_RNA_0008_23H5VFLT4_s19.Aligned.sortedByCoord.out.vcf
Generate Data Set from .
using this bed file : /usr/local/NGSCheckMate/SNP/SNP_GRCh38_hg38_wChr.bed