Question: Getting haplotypes from a VCF file
gravatar for gkuffel22
3.6 years ago by
United States
gkuffel22170 wrote:

Hi all,

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?

snps vcftools haplotypes • 2.1k views
ADD COMMENTlink modified 3.6 years ago by Jennifer Hillman Jackson25k • written 3.6 years ago by gkuffel22170
gravatar for Jennifer Hillman Jackson
3.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:


This tool is requiring SAMtools indexes for the reference genome. This must be supplied on the file system itself for built-in genomes. The index and the associated ".loc" file. You can create this again using a Data Manager from the Main Tool Shed or rearrange the data so that the indexes and loc file are available to Galaxy. More instructions for setting up reference genomes for tools is in the Galaxy wiki:

Take care, Jen, Galaxy team

ADD COMMENTlink written 3.6 years ago by Jennifer Hillman Jackson25k
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