关于CNV的注释评估

We can run EvaluateCNV to produce recall and precision metrics for Dragen-CNV.

https://github.com/Illumina/canvas

Download the standard (NA12878) CNV data from DGV database(>50bp).

http://dgv.tcag.ca/dgv/app/home

We can run VCAT to produce recall and precision metrics for SNV and Indel.

https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/variant-calling-assessment-tool.html

基于CNV的注释数据库：

https://decipher.sanger.ac.uk
http://cnvcalc.clinicalgenome.org/cnvcalc/

基于clinvar的CNV数据库注释：

（关注pathogenic/ probably pathogenic去掉 “likely benign,” and “benign"保留VUS, variant of unknown significance）

https://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz

对于关联基因的筛选应包含：
OMIM (Online Mendelian Inheritance in Man）以及ACMG list 56 medically actionable genes

拷贝数变异常用的软件：CoNIFER

http://conifer.sourceforge.net/index.html

if combine SNV and CNV analysis, the SNV and CNV must be minor allele frequency ≤1% in population databse. Or For each clinical case CNVs with a population frequency higher than 10% (~5% allele frequency) are removed from the interpretation call set.

关于CNV的一些说明可参考：

https://blog.goldenhelix.com/annotation-education-series-final-chapter-cnv-annotations/