I have been trying to convert a VCF file downloaded from 1000genomes (VCF v4.1) using this tool. However, I keep getting the error message Fatal error: Exit code 1 ()
unable to find FASTA index entry for '22”
I am using the human hg19 reference genome.
Our ultimate goal is to get phased data from 1000genomes in a FASTA format in order to calculate Tajima's D and Fay and Wu's H (measures to identify recent selective sweeps) on the sequences we are interested in.
I am new to this field, any help or advice in this regard would be greatly appreciated.
Tool name: VCFgenotype-to-haplotype:
Tool version: 0.0.2
Tool ID: toolshed.g2.bx.psu.edu/repos/anton/vcfgeno2haplo/vcfgeno2haplo/0.0.2
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/anton/vcfgeno2haplo