I'm confused about cnvkit batch. I ahve one normal bam and one tumor bam file(Exome SEQ).
I have a bed file to use for --targets, and flat ref text to go with it. I don't have an access file, or anti-target file. Do I need to use the access command first to create an access file or will batch do that with this command:
cnvkit.py batch Tumor.bam \ --normal Normal.bam \ --targets targets.bed \ --fasta Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa \ --output-reference my_reference.cnn \ --output-dir example/ \ --annotate fer.text
Please use the formatting bar (especially the
codeoption) to present your post better. I've done it for you this time.