problem in annotate my vcf file to SNPdb files or another vcf file ??

Question

[rastogi.suraj93]

hiii all, i am a new student in NGS field. i have a Q to ask for all. please help me to solve the problem. I have vcf file generated by snpEff tool and now I want to annotate this file to other vcf file or SNPdb ? how can I do? please suggest me suitable tools and commands.. Thanks in advance..

Answer 1

[Pierre Lindenbaum]

GATK variant annotator : https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_annotator_VariantAnnotator.php

Answer 2

[Jorge Amigo]

another quick option would be bcftools annotate: http://samtools.github.io/bcftools/bcftools.html#annotate

but if you need deeper annotation you may want to look at other more complex tools, such as ANNOVAR: http://annovar.openbioinformatics.org/