This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Database Of Human Structural Variants Enabling Vcf File Creation

Hi all,

I am trying to get hold of or create a VCF format file containing known, well validated human structural variants in order to introduce them into a reference genome. The end goal is to assess a range of SV detection tools using an unbiased, mutated dataset. Is anyone aware of a human SV database that enables download of this information in VCF format or in a format easily converted to VCF? I have done some searching but the only databases I have found don't appear to provide the 'reference' and 'mutant' sequence that would enable me to recreate the mutation in silico.

Thanks in advance.

next-gen vcf sv
• 4,980 views • link
updated by deanna.church deanna.church • written by Travis Travis

2 answers

dbVar (http://www.ncbi.nlm.nih.gov/dbvar) is a database of structural variants and provides FTP files in gvf format. You can get data by organisms/assembly or by organism/study: ftp://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/

• 23 views • link
written by deanna.church deanna.church

I'm not positive what exactly you need, but have you looked at the 1000 Genomes structural variation dataset?

"The pilot paper data directory contains vcf files for different types of structural variants both for the low coverage and trio pilot studies"

Data here: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/paper_data_sets/a_map_of_human_variation/

It looks like things are categorized by sequencing strategy and variant type, which might be what you need. They're already in VCF, as well.

• 0 views • link
written by matted matted

Apologies - I have edited the question to include "The end goal is to assess a range of SV detection tools using an unbiased, mutated dataset". Since the 1000G VCFs are largely unvalidated and based on some of the software I would like to test, it doesn't satisfy the well-validated/unbiased criteria. Furthermore, the 1000 genomes data you linked to consists of SNVs and small Indels only - I am specifically interested in larger structural variants.

• 0 views • link
written by Travis Travis

Log in to answer this question.

More posts like this