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gonzolgarcia / svpluscnv

Integrative Structural Variant analysis
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Is this package can analysis whole exome sequencing（WES）data？ #3

Open NymeriaYao opened 3 years ago

NymeriaYao commented 3 years ago

“SV calls can be inferred from discordantly aligned reads from whole genome sequencing (WGS) using different algorithms” in the introduction section， I am confused that whether CNV &SV calls from whole exome sequencing（WES）data can be analysis by this package. I only have WES data. This is really important for me. Thank you!

gonzolgarcia commented 3 years ago

Hi. This package uses two data types: cnv (segmentation data) and svc (SV calls); For WES you can obtain segmentation data with different algorithms (GATK, CNVkit, etc). Several functions in this package only require cnv (.seg) data and you will be able to use them normally. Other tools require svc (SV calls) and those typically are obtained from WGS. If you have SV calls from WES those will be sparse since non-coding and intron regions are missing; the model assumptions for shattered regions will not work in that case. Thanks for using svpluscnv Gonzalo

NymeriaYao commented 3 years ago

Thank you very much!