VCF file format
The VCF file contains the genetic data (genotypes). Hereafter a minimal example:
		##fileformat=VCFv4.1
		#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT  UNR1	UNR2	UNR3	UNR4
		chr7	123	SNP1	A	G	100	PASS	INFO	GT:DS	0/0:0.001	0/0:0.000	0/1:0.999	1/1:1.999
		chr7	456	SNP2	T	C	100	PASS	INFO	GT:DS	0/0:0.001	0/0:0.000	0/1:1.100	0/0:0.100
		chr7	789	SNP3	A	T	100	PASS	INFO	GT:DS	1/1:2.000	0/1:1.001	0/0:0.010	0/1:0.890
		
		
		A precise description of this file format can be found here. FastQTL needs at least one of the two following fields GT or DS. It uses in priority the DS field and if absent, the GT field from which it derives the required dosages. We strongly recommend to use dosages instead of fixed genotypes in order to account for imputation uncertainty.
Indexing VCF file (required)
To feed FastQTL with VCF files, you need to index them with tabix first. Hereafter, the commands that does it:
		bgzip genotypes.vcf && tabix -p vcf genotypes.vcf.gz		
		
		
		Look here for more details on Tabix and Bgzip command lines. The above command line produces a file genotypes.vcf.gz.tbi that contains the index for data.vcf.gz. These tow files need to be together in the same folder in order for FastQTL do be able to also read the index file when reading genotypes.vcf.gz.