.command.out - Workdir - NFCORE_RNAFUSION:RNAFUSION:RNA_CONTAMINATION_DETECTION_WORKFLOW:NGSCheckMATE (A673_FFPE_RNA_0001_B23LG7FLT4_3)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/3d2f3fd455e65cb938e1e90db550d5/.command.out
Size: 457 bytes
Task: NFCORE_RNAFUSION:RNAFUSION:RNA_CONTAMINATION_DETECTION_WORKFLOW:NGSCheckMATE (A673_FFPE_RNA_0001_B23LG7FLT4_3)
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 A673_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam | bcftools call -c > ./A673_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.vcf
Generate Data Set from .
using this bed file : /usr/local/NGSCheckMate/SNP/SNP_GRCh38_hg38_wChr.bed