I have a local
vcf file on my computer (it is actually the full chromosome 22). I would like to subset it in regions. I know
tabix can do it, but I can't find the way...
When I use tabix to connect to the ftp server there is no problem; I easily get the vcf file. But doing it locally, even if I download and put in the same folder the proper index
.tbi file, I get nothing.
This is the command I am using:
/home/peixe/tabix-0.2.6/tabix -fh -p vcf ALL.chr22.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz 22:1500000-1600000
But I am only getting an empty vcf file. In the tabix help manual, it does not not provide any tip about it...
Does anyone know a way to do it?