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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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some suggestions #26

Open panxiaoguang opened 1 year ago

panxiaoguang commented 1 year ago

  1. Sometimes after running AA and getting ecDNAs, we also want to find some somatic mutations or allele-based CNA and so on, so the RG tag in bam is mostly important ! In order to reuse the bam file from prepareAA, what about adding the function for adding RG tag to the "bwa mem" step ?

  2. I think the results from CNVkit can also be reused for the downstream analysis, so what about adding the information about genes to the "cnvkit batch" step?

jluebeck commented 1 year ago

Hi,

Thank you for the suggestions. I can certainly look in to adding both of these features in the next week or so, time permitting.

Jens

panxiaoguang commented 1 year ago

Hi,

Thank you for the suggestions. I can certainly look in to adding both of these features in the next week or so, time permitting.

Jens

Thank you so much !