Question: Need help with "VCFgenotype-to-haplotype:" tool
0
gravatar for page2
3.9 years ago by
page20
page20 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: • 1.3k views
ADD COMMENTlink modified 3.9 years ago by Jennifer Hillman Jackson25k • written 3.9 years ago by page20
0
gravatar for Jennifer Hillman Jackson
3.9 years ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 3.9 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 156 users visited in the last hour