I have 30 isolates, of these I need to know from each how many synonyms and non-synonyms SNPs I have. Is there a faster way to count without having to be one by one? These isolates had a high number of SNPs.
PS: They are grouped into a single vcf file.
Sureshkumar v.
Ingrid Moura
In BrowseVCF, You can upload single vcf of multiple samples. Lets try this.
1. BrowseVCF (https://github.com/BSGOxford/BrowseVCF/releases)
Many tools are available for this.
2. SNPGenie (https://github.com/chasewnelson/SNPGenie)
3. SnpEff (http://snpeff.sourceforge.net/)
4. VEP (http://asia.ensembl.org/info/docs/tools/vep/index.html)
5. ANNOVAR (http://annovar.openbioinformatics.org/en/latest/user-guide/gene/)
Hope this will help you.
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