confused about how to run pipeline

Question

[andrew.lamb]

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

Thanks!

[h.mon]

Hello andrew.lamb,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

Answer 1

[Tm]

You do not require access or antitarget file, because batch command runs all necessary subcommands to generate access and antitarget file.

Here they have mentioned, which subcommands are executed while using batch command.

[Chip]

I think there's an error in the documentation because it shows that you have to pass an access file but first you need to run cnvkit.py access to create it. Do what Paul suggests in his answer.

Answer 2

[Paul]

Hi,

first please create your access file (need to download exclude regions file):

cnvkit.py access hg38.fa -x excludes.bed -o access-excludes.hg38.bed

Then you can use batch command:

cnvkit.py batch --target-avg-size 70 -p 12 TUMOR/*.bam --normal NORMAL/*.bam --targets capture_region.bed --fasta hg38/genome.fa --access access-excludes.hg38.bed --output-reference try_reference_bed_70.cnn --output-dir output_splitted_bed_70

You can set up target average size - default is I think 200.

Paul.