Vcf File For Reference (Exome Sequencing)

Question

[Pierre Lindenbaum]

I'm currently designing a workflow to analyze some exome sequencing data (VCF).

Now, I'd like to test this workflow to test it against a 'reference' VCF.

I want to check if my workflow can retrieve the gene(s) that would have been previously found to be involved in a genetic disease (and published )

Do you know where I could find this kind of public VCF ?

Thanks.

Pierre

(Note: I have the feeling I already asked this kind of question before but can't retrieve it. May be, I asked it on tweeter)

Answer 1

[Zhidkov]

Hi, (just in case if you missed it) there is a 1000 genomes project database where you can find VCF files: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20101123/interim_phase1_release/

more data can be found at: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/release/2010_07/

Ilia

[Pierre Lindenbaum]

Thanks , but I'm looking for some VCF files where it is known that there is somewhere a mutation causing a genetic disease.

[Jeremy Leipzig]

someone here recommended the Jay Shendure proof of concept 12 exome Freeman-Sheldon syndrome data but I cannot find the VCFs for that, if they exist

Answer 2

[Biomed]

The best resources for this kind of data are OMIM(public) and HGMD(proprietary) but neither comes in vcf format. You may want to parse these databases into a vcf file if that's the only format you want to work with.

[Laura]

If you have rs numbers from either of these resources though you could then get the vcfs from dbSNP ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/v4.0/

Answer 3

[Travis]

I'm wondering if the Annovar program has any ability like this or if it could easily be altered to perform what you mention? From my limited exposure it sounds appropriate and seems quite customisable.

Answer 4

[Rm]

SNPs3D has list of Candidate human Disease associate Genes and SNPs. I am afraid, You might need to parse it to vcf format