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virajbdeshpande / AmpliconArchitect

AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.
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CNV need to consider sample purity and ploidy? #128

Open Bio-LiHe opened 1 year ago

Bio-LiHe commented 1 year ago

Hi，

when I call CNVs using CNVkit, need to consider sample purity and ploidy to caculate absolute copy number?

jluebeck commented 1 year ago

Hi,

Excellent question. Users do not not need to provide sample purity and ploidy estimates to CNVKit in order to use it for CNV seed generation. AmpliconArchitect is not designed for single-cell or subclonal event detection. Rather, it identifies ecDNA and other focal amplifications in bulk by comparing coverage in seed regions against background non-amplified regions.

Just in case you are not aware, there is a pipeline for running the preparation and AA steps together here: https://github.com/jluebeck/AmpliconSuite-pipeline

Thanks, Jens