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zhqingit / giremi

GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.
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SNV list: How to get the Giremi input file from the vcf file #48

Closed mt831 closed 6 years ago

mt831 commented 6 years ago

Hi, I've get the SNV list by using STAR and GATK. But the output vcf file don't have the information like the name of the gene harboring this SNV, strand of SNV and whether the SNV belongs to dbSNP. So I just want to know if I need to use annotation tools like annovar, SnpEff to annotate the vcf file and then try get the Giremi input file.

Thanks.

mt831 commented 6 years ago

I used SnpEff to annotate vcf file and then used python script to get the SNV list.