write_vcf: Create VCFv4.3 file

In jendelman/polyBreedR: Genomics-assisted breeding for polyploids (and diploids)

Create VCFv4.3 file

Description

Create VCFv4.3 file

Usage

write_vcf(filename, fixed, geno, other.meta = NULL)

Arguments

filename	VCF file name
fixed	character matrix with 8 columns: CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO
geno	named list of genotype matrices, see Details
other.meta	optional, other metadata (without ##) besides INFO and FORMAT keys

Details

Several standard INFO key are recognized: ##INFO=<ID=REF,Number=A,Type=Character,Description=\"Array allele (A/B) in reference genome\"> ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> ##INFO=<ID=DP.AVG,Number=1,Type=Float,Description="Average Sample Depth"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> ##INFO=<ID=AB,Number=1,Type=Float,Description="Allelic Bias"> ##INFO=<ID=SE,Number=1,Type=Integer,Description="Sequencing Error (PHRED)"> ##INFO=<ID=OD,Number=1,Type=Integer,Description="OverDispersion (PHRED)"> ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency"> ##INFO=<ID=AF.GT,Number=A,Type=Float,Description="Allele Frequency based on GT"> ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">" ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles">" Every element of geno is m x n matrix (m variants, n samples), e.g., AD, GT. The FORMAT field is created from the order and names of geno. Sample names taken from colnames of geno. Metadata for geno is generated from the names of the list: ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allele Depth"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Sample Depth"> ##FORMAT=<ID=DS,Number=1,Type=Float,Description="Posterior Mean Dosage"> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">

Any additional metadata should be included without the ## prefix.

jendelman/polyBreedR documentation built on Jan. 5, 2025, 12:13 a.m.