DEploid.utils (version 0.0.1)

extractCoverageFromVcf: Extract VCF information

Description

Extract VCF information

Usage

extractCoverageFromVcf(filename, samplename)

Value

A dataframe list with members of haplotypes, proportions and log likelihood of the MCMC chain.

• CHROM SNP chromosomes.

• POS SNP positions.

• refCount reference allele count.

• altCount alternative allele count.

Arguments

filename

VCF file name.

samplename

Sample name

See Also

• extractCoverageFromVcf

• extractCoverageFromTxt

Examples

vcfFile = system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid.utils")
vcf = extractCoverageFromVcf(vcfFile, "PG0390-C")