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Question: Need help with "VCFgenotype-to-haplotype:" tool
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gravatar for page2
4.2 years ago by
page2 • 0
page2 • 0 wrote:

Hello,

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

 
vcfgenotype-to-haplotype: • 1.4k views
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modified 4.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.2 years ago by page2 • 0
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gravatar for Jennifer Hillman Jackson
4.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This looks like a reference genome mismatch issue.
http://wiki.galaxyproject.org/Support#Reference_genomes

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 COMMENT • link written 4.2 years ago by Jennifer Hillman Jackson ♦ 25k
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