fastqtl ERROR: No genotypes in this region

Question

[zsl_picb]

Hello everyone, I am runing fastQTL as bellow:

fastQTL --vcf ./tt.genotype.vcf.gz --bed ./tt.tpm.tss.qn.bed.gz --window 1e6 --maf-threshold 0.01 --ma-sample-threshold 10 --interaction-maf-threshold 0 --cov ./tt.sample_info.t --permute 1000 10000 --chunk 7 100 --out ./eqtls_fastqtl_chunk007.txt.gz --log ./eqtls_fastqtl_chunk007.log

but encount:

Fast QTL

• Authors : Olivier DELANEAU, Halit ONGEN, Alfonso BUIL & Manolis DERMITZAKIS
• Contact : [e-mail]
• Webpage : http://fastqtl.sourceforge.net/
• Version : v2.184_gtex

Perform permutation based analysis (used to calculate corrected p-values for MPs)

• Perform between 1000 and 10000 permutations
• Random number generator is seeded with 1668133454
• Considering variants within 1e+06 bp of the MPs
• Using minor allele frequency threshold = 0.0100
• Using minor allele sample threshold = 10
• Using INFO field AF threshold = 0.0000
• Applying interaction MAF AF threshold = 0.0000
• Chunk processed 7 / 100

Scanning phenotype data in [./tt.tpm.tss.qn.bed.gz]

• 21765 phenotypes

Reading phenotype data in [./tt.tpm.tss.qn.bed.gz]

• region = 1:151047751-159945613
• 516 samples included
• 220 phenotypes included

Reading genotype data in [./tt.genotype.vcf.gz] in VCF format

• region = 1:150047751-160945613
• 516 samples included
• 0 sites included

ERROR: No genotypes in this region: 1:151047751-159945613

how to solve this? any comments would be appreciated!

[h.mon]

FastQTL is complaining there are no variants in the region you specified. What does tabix ./tt.genotype.vcf.gz 1:151047751-159945613 | tail shows? You need tabix (from SAMtools / BCFtools / HTSlib, I don't remember currently which package hold tabix) and maybe you will need to index the vcf with tabix -p ./tt.genotype.vcf.gz.