Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: How can I get the HaplotypeCaller tool added to my Galaxy
0
gravatar for cg2p
7 weeks ago by
cg2p • 0
cg2p • 0 wrote:

Hi Would it be possible to add HaplotypeCaller into Galaxy - it is described as the bestprocatice tool by GATK
galaxy • 81 views
ADD COMMENT • link •
modified 7 weeks ago • written 7 weeks ago by cg2p • 0
0
gravatar for Jennifer Hillman Jackson
7 weeks ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

All currently wrapped versions of GATK tools are deprecated due to the outdated versions and/or licensing issues.

There are plans to wrap the latest release but that is still a work-in-progress. Use Freebayes/VCFtools instead. Workflow examples are in the Galaxy tutorials: https://galaxyproject.org/learn/

Thanks! Jen, Galaxy team
ADD COMMENT • link written 7 weeks ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for cg2p
7 weeks ago by
cg2p • 0
cg2p • 0 wrote:

Freebayes/VCFtools I want to use the VCF files to identify SNPs in control and variant sample populations. What is the best tool for doing this - I can generate the SNPs using Freebayes but I have not found a workflow example for this next step and it is very frustrating!!

Thank you for your response Carol
ADD COMMENT • link written 7 weeks ago by cg2p • 0

Genotypes generated using Freebayes can be converted to Haplotypes with the tool

  • NGS: VCF Manipulation > VCFgenotype-to-haplotype: Convert genotype-based phased alleles into haplotype alleles
ADD REPLY • link written 7 weeks ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 181 users visited in the last hour