Comparing vcf with dbSNP

Question

[cvu]

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

Answer 1

[poisonAlien]

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

[cvu]

can we use samtools or GATK for this?

[Ashutosh Pandey]

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

[Brad Chapman]

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

Answer 2

[cristianrohr768]

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

Answer 3

[Bert Overduin]

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).