Question: Problem with Refreence Genome in Gatk Tools
0
gravatar for mltlbrt
4.0 years ago by
mltlbrt10
United States
mltlbrt10 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

 

ADD COMMENTlink modified 3.2 years ago by regina.casanova.900 • written 4.0 years ago by mltlbrt10
0
gravatar for Jennifer Hillman Jackson
4.0 years ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 4.0 years ago by Jennifer Hillman Jackson25k
0
gravatar for regina.casanova.90
3.2 years ago by
regina.casanova.900 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 COMMENTlink written 3.2 years ago by regina.casanova.900

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 REPLYlink written 2.5 years ago by madi.naima0
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