How to parse the output file of snpEFF

Question

[yoser4]

Hello everyone. I have a vcf file annotated with snpEFF (the input file for snpEFF was extracted from a snp vcf file of 99 samples, and I picked a CDS region of a gene of interest). Now I want to do the following two aspects:

1. Statistical variation (such as synonymous mutation or missense mutation) in the vcf file output by snpEFF
2. The vcf file output by snpEFF generates its own base sequence for each sample (or it is better to generate amino acid sequence directly) --- Here I want to draw an evolutionary tree through the amino acid sequence.

Please tell me what you think, any help is greatly appreciated.

Answer 1

[prasundutta87]

Check out Snpsift filter command: https://pcingola.github.io/SnpEff/ss_filter/

You can do a variety of custom filters according to your need.