I've generated vcf file using samtools. now how do i compare my SNPs with dbSNP ?
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cvu
3 answers
Assuming you have dbSNP in VCF format you can use vcf-compare
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poisonAlien
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:
http://www.ncbi.nlm.nih.gov/books/NBK9777/#FTP.how_do_i_extract_information_from_db
You can add dbSNP annotations with GATK using VariantAnnotator with the --dbsnp flag:
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Brad Chapman
You can annotate with dbSNP ids using SnpSift, and then with the effects of the variants using SnpEff.
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cristianrohr768 •
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).
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