SNP database alignment

Question

[tnazlin22]

Hi there,

I'm Lynn from Malaysia. I need help here. I have a large file of SNP data from whole genome sequencing (gigabite). Is it possible for me to align the SNP that I have with the SNP database available? Is there any suggestion on what software that can fulfill my needs?

Thank you in advance..

[Ashutosh Pandey]

I assume by 'align' you meant to compare with existing SNP database. Right? If your already have a existing database in vcf format, you can use vcf-compare. You can also use snpEff and GATK VariantAnnotator. Check this relevant post: Comparing vcf with dbSNP

Answer 1

[Ruru]

You can use Variant Effect Predictor (VEP) in ENSEMBL. Presume if your species has a reference genome or closely related genome. Manipulate your vcf format. Good luck.