Question: Gene Set Analysis Software That Takes A Vcf As Input
1
gravatar for potassiumiodide0990
6.6 years ago by
United States
potassiumiodide099080 wrote:

I have generated a vcf file, and was wondering if there is any gene set analysis server/software that is available that takes the vcf file as an input. Even otherwise, what are the other gene analysis softwares available? Is cytoscape good enough?

vcftools • 2.4k views
ADD COMMENTlink modified 6.6 years ago by Alex Reynolds31k • written 6.6 years ago by potassiumiodide099080

Should the tool take into account the genotypes, or just the list of SNPs?

ADD REPLYlink written 6.6 years ago by Giovanni M Dall'Olio27k

Hi Giovanni... just the list of SNPs will do...

ADD REPLYlink written 6.6 years ago by potassiumiodide099080

Just keep in mind that gene set analysis softwares have a model for what is "expected"; this background model is critical for determining the "significance" of enrichment. This model may or may not be appropriate for your data, so be careful in interpreting any results, no matter what tool you use.

ADD REPLYlink modified 6.6 years ago • written 6.6 years ago by Sean Davis26k
0
gravatar for Giovanni M Dall'Olio
6.6 years ago by
London, UK
Giovanni M Dall'Olio27k wrote:

I am not aware of any Ontology Enrichment tool able to read VCF files directly, but you can convert the file to BED (e.g. see this discussion in SeqAnswers), and then use GREAT from the Bejerano┬┤s lab.

The advantage of GREAT is that it is designed for point positions and small regions, so it first gives you the list of the closests genes to each SNP, and then does an enrichment analysis on many databases.

I suspect that an alternative way to converting the VCF file to BED is to upload the VCF to the UCSC browser as a custom track, then go to the Tables function, and then select your custom track and send it to GREAT directly. However, this method also requires to convert the VCF to a VCF-tabix format (see the instructions here), so maybe it's not worth the effort.

ADD COMMENTlink written 6.6 years ago by Giovanni M Dall'Olio27k
0
gravatar for Alex Reynolds
6.6 years ago by
Alex Reynolds31k
Seattle, WA USA
Alex Reynolds31k wrote:

The vcf2bed conversion script in BEDOPS can pull out single-nucleotide variants:

$ vcf2bed --snvs < foo.vcf > foo.snvs.bed

Once you have it in BED format, you can do all kinds of set and map operations with other BEDOPS tools.

ADD COMMENTlink modified 6.6 years ago • written 6.6 years ago by Alex Reynolds31k
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