batch command parameter usage

[enes-ak]

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?

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

[etal]

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 ...

[etal]

Answered: use --normal once followed by all normal BAMs. Closing as answered — please reopen, or open a new issue, if a concrete problem remains.

For general usage questions, we now use GitHub Discussions (Q&A): https://github.com/etal/cnvkit/discussions