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Published 20 hours ago • verified publisher icon AmpliconSuite

some suggestions

Open SeqCrafter opened this issue 3 years ago • 2 comments

  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?

SeqCrafter avatar Sep 02 '22 04:09 SeqCrafter

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

jluebeck avatar Sep 02 '22 05:09 jluebeck

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 !

SeqCrafter avatar Sep 02 '22 06:09 SeqCrafter