I am trying to run tumor-normal analysis for somatic pipeline in Parabricks
However, parabricks somatic pipeline does not align normal fastq and I cannot find any normal.bam file in the output folder that I specified…
Moreover the generated VCF file has the size too big to be the one that generated by tumor-normal analysis
Please help me with this issue
My command line was: "sudo pbrun somatic --ref inputs/refs/reference.fasta --in-se-tumor-fq inputs/tumor/VT-tumor-gz_S1_L001_R1_001.fastq.gz --out-vcf outputs/output.vcf --out-tumor-bam outputs/tumor.bam --in-se-normal-fq inputs/normal/VT-normal-gz_S1_L001_R1_001.fastq.gz --out-normal-bam outputs/normal.bam "
Thank you