benchmarking/validation tools for CNVs
3
1
Entering edit mode
7.6 years ago
Jackie ▴ 70

Are there good benchmarking/validation tools for CNVs? By 'benchmarking/validation', I mean, you feed the tool a truth set and the CNVs called by a CNV caller, then the tool will output something like the sensitivity and specificity of the CNV caller.

Thanks!

CNV validation benchmarking truth set • 3.6k views
ADD COMMENT
0
Entering edit mode

It depends on the data you use. For WGS, check out the GiaB (https://www.nature.com/articles/s41587-020-0538-8.epdf) HG002 truth set. There are also tools: truvari, SVanalyzer that compare the vcfs and report Precision/Recall metrics.

For WES, panels, you can try ICR96 dataset (you will need to request): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5473400/

HTH

ADD REPLY
0
Entering edit mode
6.7 years ago
Paul ★ 1.5k

Hi, did you try Ximmer ?? It is "Ximmer is a tool designed to help users of exome and targeted genomic sequencing data accurately detect and interpret copy number variants (CNVs). Ximmer is not a copy number detection tool itself. Rather, it is a framework for running other copy number detection tools and interpreting their results"

ADD COMMENT
0
Entering edit mode
4.4 years ago
jpuntomarcos ▴ 50

Hi,

The framework CNVbenchmarkeR was implemented with this purpose. Currently, it supports DECoN, CoNVaDING, panelcn.MOPS, ExomeDepth and CODEX2 tools. Hope it helps.

We used it to benchmark CNV detection tools for targeted NGS data (paper)

ADD COMMENT
0
Entering edit mode
4.4 years ago

I would say comparison with Genome-in-a-Bottle results for a well-known human sample would be the best benchmark.

ADD COMMENT

Login before adding your answer.

Traffic: 821 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6