Question: Comparing vcf with dbSNP
0
gravatar for cvu
3.3 years ago by
cvu110
India
cvu110 wrote:

I've generated vcf file using samtools. now how do i compare my SNPs with dbSNP ?

alignment snp next-gen assembly • 3.2k views
ADD COMMENTlink modified 3.3 years ago by cristianrohr76820 • written 3.3 years ago by cvu110
3
gravatar for poisonAlien
3.3 years ago by
poisonAlien2.4k
Asgard
poisonAlien2.4k wrote:

Assuming you have dbSNP in VCF format you can use vcf-compare

ADD COMMENTlink written 3.3 years ago by poisonAlien2.4k

can we use samtools or GATK for this?

ADD REPLYlink written 3.3 years ago by cvu110

Samtools and GATK can't be used to add dbSNP rsID information to vcf file. Either you use vcf-compare as suggested above or your own script to add rsids to the vcf file. You will have to download dbSNP data from NCBI.

Check these links:

Snp Rsid By Location?

http://www.ncbi.nlm.nih.gov/books/NBK9777/#FTP.how_do_i_extract_information_from_db

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by Ashutosh Pandey11k

You can add dbSNP annotations with GATK using VariantAnnotator with the `--dbsnp` flag:

http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_VariantAnnotator.html


 

ADD REPLYlink written 3.3 years ago by Brad Chapman9.1k
2
gravatar for cristianrohr768
3.3 years ago by
Spain
cristianrohr76820 wrote:

You can annotate with dbSNP ids using SnpSift, and then with the effects of the variants using SnpEff

 

http://snpeff.sourceforge.net/

ADD COMMENTlink written 3.3 years ago by cristianrohr76820
1
gravatar for Bert Overduin
3.3 years ago by
Bert Overduin3.6k
Edinburgh Genomics, The University of Edinburgh
Bert Overduin3.6k wrote:

If your goal is to find out whether your SNPs are known or novel, you can also think of using the Ensembl Variant Effect Predictor (VEP).

ADD COMMENTlink written 3.3 years ago by Bert Overduin3.6k
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