I have ran a variant analysis pipeline on some Illumina paired end data. My workflow included BWA, FreeBays, and VCF manipulation. The user is requesting haplotype block information (which variants are inherited together/on the same strand). It seems that there is a perfect tool for this under VCF: Manipulation called VCFgenotype-to-haplotype. When I try to run this tool I do not get the expected output and get the following message: "index file local ref.fa.fai not found, generating..." however the file never gets generated. I have this file available because it is created automatically when I load my reference genome.fasta into IGV. The only problem is the tool does not take this fai index file as an input. Any suggestions?