How to convert GEN or .gen format from impute.me to vcf on windows 10?

Question

[chrisbab123456]

I tried for days to convert a gen file to vcf but it did not work. I am a beginner so i don't know what are in vcf files and gen files or how they work. I saw some tools like samtools or bcftools but it's on linux, i saw other tools but require linux or mac as well. I tried with plink but it says that it need a .sample file and i don't know what is that .sample file. I tried an other tool, fcgene but it gave me an error when i tried to convert to vcf. Do you guys know a simple tool to convert a gen file to vcf or even convert it to 23andme format?

[chrisbab123456]

I am a beginner and not a geneticist and i don't know what are gen and vcf files. There is a tool named dnakitstudio that convert a vcf to 23andme and other dna compagny formats. I can't do anything with that gen file. I want a simple method to convert a gen file to vcf or 23andme format. I searched some tools like bcftools or samtools or many other and all of them require linux or mac. I tried fcgene and it gave a a sample file but in plink it says invalid first header line in .sample file. Is there a tutorial or a way to see what is that .sample file?

Answer 1

[lassefolkersen]

Hi chrisbab123456 Try going to www.impute.me/downloads There's a (still) undocumented / unreleased conversion mechanism, that can take the basic .gen file output and automatically convert to other formats, including vcf. Please let me know if the upload functionality acts up - we've had some reports of that, and it happens before any error logs are made so it's difficult to follow up on. If you use the unmodified raw data zip you got in your results mail, however, there shouldn't be a problem.