Genotype file format conversion between Variant Call Format (VCF), PED/MAP, HapMap and the general genotype file format (see below).
https://github.com/njau-sri/gconv/releases
usage: gconv [options]
--geno <> Input legacy genotype file
--hmp <> Input HapMap genotype file
--out <> Output file with format suffix (.vcf/.ped/.hmp/.geno)
--ped <> Input PLINK ped file (map file has same basename)
--vcf <> Input VCF genotype file
--sort sorting loci in ascending chromosome position order
Each row is a marker, each column is an individual. The first row contains column names and individual names. The first three columns are marker names, chromosome labels and genome positions, respectively.
-
arbitrary allele code:
number
character
string
-
supported allele separator:
space
tab
/
:
-
supported missing genotype:
N
-
.
?
Locus | Chromosome | Position | Ind1 | Ind2 |
---|---|---|---|---|
Mk1 | 1 | 100 | 630/630 | 909/909 |
Mk2 | 1 | 200 | 557/711 | 711/711 |
Mk3 | 1 | 300 | 445/445 | 445/668 |
Mk4 | 2 | 1001 | 307/307 | 340/340 |
Mk5 | 2 | 1002 | 264/273 | 264/264 |