Question: How can I get the HaplotypeCaller tool added to my Galaxy
0
gravatar for cg2p
5 weeks ago by
cg2p0
cg2p0 wrote:

Hi Would it be possible to add HaplotypeCaller into Galaxy - it is described as the bestprocatice tool by GATK

galaxy • 70 views
ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by cg2p0
0
gravatar for Jennifer Hillman Jackson
5 weeks ago by
United States
Jennifer Hillman Jackson25k 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All currently wrapped versions of GATK tools are deprecated due to the outdated versions and/or licensing issues.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 COMMENTlink written 5 weeks ago by Jennifer Hillman Jackson25k
0
gravatar for cg2p
5 weeks ago by
cg2p0
cg2p0 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 COMMENTlink written 5 weeks ago by cg2p0

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 REPLYlink written 5 weeks ago by Jennifer Hillman Jackson25k
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