List of CNV (copy number variation) regions in the human genome

Question

[abascalfederico]

Does anyone know where could I find a comprehensive list of human CNV regions? I am working with 1000G variants and want to filter out variants within CNV regions, to see whether some pattern change or not.

Thanks,
Federico

Answer 1

[trausch]

The 1000 Genomes Consortium recently published an integrated SV/CNV map for the 1000 Genomes phase 3 data:

http://www.nature.com/nature/journal/v526/n7571/full/nature15394.html

As a VCF file:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/integrated_sv_map/ALL.wgs.integrated_sv_map_v2.20130502.svs.genotypes.vcf.gz

Alternatively, Decipher also has a population CNV map in tab-delimited format:

https://decipher.sanger.ac.uk/files/downloads/population_cnv.txt.gz

[abascalfederico]

This is really helpful. Thank you!

I have also found the 1000G accessibility genome masks, which may help to retain only high quality variants: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/accessible_genome_masks/README_20120824_accessibility_mask_bed_files