Question: Need help with "VCFgenotype-to-haplotype:" tool
gravatar for page2
3.9 years ago by
page20 wrote:


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 URL:


vcfgenotype-to-haplotype: • 1.3k views
ADD COMMENTlink modified 3.9 years ago by Jennifer Hillman Jackson25k • written 3.9 years ago by page20
gravatar for Jennifer Hillman Jackson
3.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:


This looks like a reference genome mismatch issue.

Try using the 'hg_g1k_v37' genome instead of 'hg19'. That is the 1000 genomes human reference genome used by GATK.

Best, Jen, Galaxy team

ADD COMMENTlink written 3.9 years ago by Jennifer Hillman Jackson25k
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