vcf {LEA} | R Documentation |
vcf
format descriptionDescription of the vcf
format.
The vcf
format can be used as an input format
for genotypic matrices in the functions snmf
,
lfmm
, and pca
.
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
Eric Frichot
vcf2geno
vcf2lfmm
geno
lfmm
ped
ancestrymap