geno4sd.utils.snpeff_tools module

Summary

Functions:

cancer_analysis	Function to run SnpEff cancer analysis annotation mode
download_genome	Function to download genome
parse_vcf	Function to parse vcf into panda dataframe

Reference

download_genome(genome)

Function to download genome

Params genome

name of genome to download

cancer_analysis(inputvcf, outputvcf, genome='GRCh38.p13')

Function to run SnpEff cancer analysis annotation mode

Params inputvcf

<string> path to input vcf

Params outputvcf

<string> path to output vcf

Params genome

<string> Genome version to use. Be sure of have already downloaded it. Default is “GRCh38.p13”

parse_vcf(inputvcf)

Function to parse vcf into panda dataframe

Params inputvcf

<string> path to input vcf

Returns

<dataframe> parsed object