AmpliconSuite/AmpliconSuite-pipeline

some suggestions

panxiaoguang opened this issue · 2 comments

panxiaoguang commented

  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

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

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 !