Copy Number Variations in Whole Exome Sequencing

Question

[victorrg]

Hi everyone!

I'm practically new to bioinformatics, currently working on a project finding germline pathogenic CNV related to eye dystrophies. Since the star I tried to work on R, realised that most tools I'll be working on are available at Galaxy. However, the annotation tools we use (XCNV and CNVxplorer) doesn't allow heavy input files.

How do we build a database from our CNVs or how do we integrate them in another database?

We have over 600 exomes, is there a pipeline that can manage to process them quickly?

Is there an annotator that can handle several CNV calls?

Is it still recomendable to be working stil in galaxy or should we consider to work in another cloud service platform?

Thank you.

Answer 1

[Pierre Lindenbaum]

realised that most tools I'll be working on are available at Galaxy.

and most tools you need are available on the linux command line...

How do we build a database from our CNVs

you "just" merge the CNV into a big VCF file e.g: https://github.com/fritzsedlazeck/SURVIVOR

or how do we integrate them in another database?

you merge/intersect with another VCF (see bedtools, bcftools...)

Is there an annotator that can handle several CNV calls?

VEP: https://www.ensembl.info/2020/03/27/cool-stuff-the-ensembl-vep-can-do-annotating-structural-variants/

https://github.com/brentp/vcfanno

....