Parameter for cnvkit in Readme need change

AmpliconSuite / AmpliconSuite-pipeline

A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.

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Parameter for cnvkit in Readme need change #14

Closed Si-Nan closed 3 years ago

Si-Nan commented 3 years ago

Hello,

I notice that you have integrated cnvkit into docker and we can start PAA with only sorted bam. It will use cnvkit in docker for seed generation with option --run_cnvkit. It has changed in software but not change in readme. I think it should change to this, right?

/path/to/PrepareAA/PrepareAA.py -s sample_name  -t number_of_threads --run_cnvkit  --sorted_bam sample.cs.rmdup.bam [--run_AA]

Thanks for your work to make this pipeline !

jluebeck commented 3 years ago

Hi,

Great suggestion - I updated the docker section of the readme to provide an example command for using the docker script with --run_cnvkit. The main script still requires the user to specify the the location of CNVKit.

Please let me know if there are other things I can make more clear.

Best regards, Jens