GEN-SAMPLE

GEN-SAMPLE to PED-MAP

./gtool  -G --g input_file.gen --s input_file.sample --ped output_file.ped --map output_file.map

GEN-SAMPLE to RAW

./gtool  -G --g input_file.gen --s input_file.sample --ped output_file.ped --map output_file.map
./plink --file output_file --recodeA --out output_file2

GEN-SAMPLE to BED-BIM-FAM

./gtool  -G --g input_file.gen --s input_file.sample --ped output_file.ped --map output_file.map
./plink --file output_file --make-bed --out output_file2

GEN-SAMPLE to VCF

./gtool  -G --g input_file.gen --s input_file.sample --ped output_file.ped --map output_file.map
./plink --file output_file --recode vcf --out output_file2

GEN-SAMPLE to 23andme

./gtool  -G --g input_file.gen --s input_file.sample --ped output_file.ped --map output_file.map
./plink --file output_file --recode vcf --out output_file2
1. Convert VCF to 23andme --> VCFto23andme()
See VCFto23andme

GEN-SAMPLE to AncestryDNA

./gtool  -G --g input_file.gen --s input_file.sample --ped output_file.ped --map output_file.map
./plink --file output_file --recode vcf --out output_file2
1. Convert VCF to 23andme --> VCFto23andme()
See VCFto23andme
2. Convert 23andme to AncestryDNA --> 23andmetoAncestryDNA()
See 23andmetoAncestryDNA

GEN-SAMPLE to HAPS-LEGEND-SAMPLE

./gtool  -G --g input_file.gen --s input_file.sample --ped output_file.ped --map output_file.map
./plink --file output_file --recode vcf --out output_file2
bcftools convert output_file2.vcf  -h  output_file3