seqminer (version 0.1)

readVCFToListByGene: Read a gene from VCF file and return a genotypes matrix

Description

Read a gene from VCF file and return a genotypes matrix

Usage

readVCFToListByGene(fileName, geneFile, geneName,
    annoType, vcfColumn, vcfInfo, vcfIndv)

Arguments

fileName

input VCF file (Bgzipped, with Tabix index)

geneFile

a text file listing all genes in refFlat format

geneName

which gene(s) to be extracted

annoType

which annotation you would like to extract

vcfColumn

which vcf columns to extract, e.g. CHROM, POS, FILTER...

vcfInfo

which tag in the INFO columns to extarct. e.g. DP, AC...

vcfIndv

which individual tag to extract, e.g. GT, GQ...

Value

• a list of genes, and each elements has specified vcfColumn, vcfinfo, vcfIndv