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Question: Problem with Refreence Genome in Gatk Tools
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gravatar for mltlbrt
4.2 years ago by
mltlbrt • 10
United States
mltlbrt • 10 wrote:

Hi,

I am attempting to run a variant call on Gatk. I used the "Validate Variants" tab first, however the reference genome list is not appearing. Shouldn't the reference file, hg19 be embedded in the software already or must I download it?

It was embedded already as a reference file when I ran the variant call in Samtools.

 

Thanks for any help

 
gatktools galaxy gatk referncegenome • 1.9k views
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modified 3.4 years ago by regina.casanova.90 • 0 • written 4.2 years ago by mltlbrt • 10
0
gravatar for Jennifer Hillman Jackson
4.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The reference genome available natively on the public Main Galaxy instance at http://usegalaxy.org is the human version from 1000 Genomes released with the GATK source kit: hg_g1k_b37

Use this for all steps in the analysis process. Mixing genomes will be problematic.
http://wiki.galaxyproject.org/Support#Reference_genomes

While these tools do permit the use of a Custom reference genome, it works best with smaller ones on Main (memory problems can come up otherwise). If you must use UCSC's hg19, then a production local or cloud Galaxy is best.
http://wiki.galaxyproject.org/Support#Custom_reference_genome
http://wiki.galaxyproject.org/BigPicture/Choices

Best, Jen, Galaxy team
ADD COMMENT • link written 4.1 years ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for regina.casanova.90
3.4 years ago by
regina.casanova.90 • 0
regina.casanova.90 • 0 wrote:

Hello Jen,

I'm facing the same problem, I can't use the reference genome even tough I have imported the right .fasta file into my history. I don't know what to do, it just says "No fasta dataset available", please guide me.
ADD COMMENT • link written 3.4 years ago by regina.casanova.90 • 0

Hi Regina I am facing exactly the same problem now, with a rasta in my history but still have the same message : "No fasta dataset available". How did you resov it?? please help ! Best, N.

ADD REPLY • link written 2.7 years ago by madi.naima • 0
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