njau-sri / gconv

Genotype file (VCF, PED/MAP, HapMap) conversions

gconv

Genotype file format conversion between Variant Call Format (VCF), PED/MAP, HapMap and the general genotype file format (see below).

Download

https://github.com/njau-sri/gconv/releases

Command line options

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

Legacy genotype file format (.geno)

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 - . ?

Example: two individuals typed at five SSR markers

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