BED file
The BED file contains the phenotypic data in a UCSC BED derived format. It is basically a BED file with one additional column per sample. Hereafter an example of 3 molecular phenotypes for 4 samples.
		#Chr	start	end	ID	UNR1	UNR2	UNR3	UNR4
		chr1	173863	173864	ENSG123	-0.50	0.82	-0.71	0.83
		chr1	685395	685396	ENSG456	-1.13	1.18	-0.03	0.11
		chr1	700304	700305	ENSG789	-1.18	1.32	-0.36	1.26
		
	
		This file is TAB delimited. Each line corresponds to a single molecular phenotype. The first 4 columns are:
- Chromosome ID [string]
- Start genomic position of the phenotype (e.g. TSS) [integer]
- End genomic position of the phenotype (e.g. TSS) [integer]
- Phenotype ID [string]
Then additional columns give phenotype quantifications for all samples. Phenotype quantifications are encoded with floating numbers. This file should have P lines and N+4 columns where P and N are the numbers of phenotypes and samples, respectively.
Indexing BED file (required)
To feed FastQTL with BED files containing phenotypes, you need to index them with tabix first. Hereafter, the commands that does it:
		bgzip phenotypes.bed && tabix -p bed phenotypes.bed.gz		
		
		
		Look here for more details on Tabix and Bgzip command lines. The above command line produces a file phenotypes.bed.gz.tbi that contains the index for data.bed.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 phenotypes.bed.gz.