vcf: 'vcf' format description

In LEA: LEA: an R package for Landscape and Ecological Association Studies

Description

Description of the vcf format. The vcf format can be used as an input format for genotypic matrices in the functions snmf, lfmm, and pca.

Details

The vcf format is described here.

Here is an example of a genotypic matrix using the vcf format with 3 individuals and 4 loci:

##fileformat=VCFv4.1 
##FORMAT=<ID=GM,Number=1,Type=Integer,Description="Genotype meta"> 
##INFO=<ID=VM,Number=1,Type=Integer,Description="Variant meta"> 
##INFO=<ID=SM,Number=1,Type=Integer,Description="SampleVariant meta"> 
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE0 SAMPLE1 SAMPLE2 
1 1001 rs0000 T C 999 . VM=1;SM=100 GT:GM 1/0:1 0/1:2 1/1:3 
1 1002 rs1111 G A 999 . VM=2;SM=101 GT:GM 0/0:6 0/1:7 0/0:8 
1 1003 notres G AA 999 . VM=3;SM=102 GT:GM 0/0:11 ./.:12 0/1:13 
1 1004 rs2222 G A 999 . VM=3;SM=102 GT:GM 0/0:11 . 1/0:13
1 1003 notres GA A 999 . VM=3;SM=102 GT:GM 0/0:11 ./.:12 0/1:13 
1 1005 rs3333 G A 999 . VM=3;SM=102 GT:GM 1/0:11 1/1:12 0/1:13 

Author(s)

Eric Frichot

See Also

vcf2geno vcf2lfmm geno lfmm ped ancestrymap

LEA documentation built on Nov. 8, 2020, 8:19 p.m.