I'm looking for tools working under windows environment with java that could be used as atlernatives to vcftools or even GATK.
I haven't seen anything similar. I have a perl script that I usually use to filter and convert vcf files into tables or fasta alignments. I think there is a command line vcftools package that does similar things, but I haven't seen anything in java.
Thank you Jonathan. I had found a website proposing linux tools (samtools, bcftools) adapted to windows (http://bow.codeplex.com/). Yet, I finally managed to use vcftools with cygwin, after I made all possible mistakes of a beginner -for instance the problem of Path for perl or tabix...-.
Alternatively, you could try the GATK and vcf tools embeded in the Galaxy environment, these are very user-friendly (http://usegalaxy.org/). They implemented most of the options of the tools, but on the other side, it implies to work on a distant server. Except if you have the possibility to have Galaxy set up on a local server, which is great !
Seeing that you are in Nantes, you would most likely benefit from the Galaxy instance at Roscoff : http://abims.sb-roscoff.fr/galaxyproject.
Good luck in your search of mutations...
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