Open enes-ak opened 2 years ago
Hello, I wanted to ask something about cnvkit batch command.
cnvkit.py batch *Tumor.bam --normal *Normal.bam \ --targets my_baits.bed --annotate refFlat.txt \ --fasta hg19.fasta --access data/access-5kb-mappable.hg19.bed \ --output-reference my_reference.cnn --output-dir results/ \ --diagram --scatter
I copied this from the documentation.
I noticed something about the --normal flag. If I add --normal flag before each normal bam file the results change. What is different between using batch command with only one --normal flag and adding --normal flag before each normal bam?
--normal
cnvkit.py batch target.bam --normal n1.bam --normal n2.bam --normal n3.bam --targets related_bed_file.bed --fasta Homo_sapiens_assembly38.fasta --access access-excludes.hg38.bed --output-reference ref.cnn --target-avg-size 100 --drop-low-coverage --output-dir /batch_res
Just use --normal once, followed by all the BAMs you want to treat as normal:
cnvkit.py batch target.bam --normal n1.bam n2.bam n3.bam --targets related_bed_file.bed ...
Hello, I wanted to ask something about cnvkit batch command.
I copied this from the documentation.
I noticed something about the
--normal
flag. If I add--normal
flag before each normal bam file the results change. What is different between using batch command with only one --normal flag and adding --normal flag before each normal bam?