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Question: Need to use hg38 as reference in GATK
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gravatar for Mei_Wu
2.3 years ago by
Mei_Wu • 0
Mei_Wu • 0 wrote:

I need to use the SNP calling tool in GATK, but I can only find hg37 as the reference under the GATK tab. Is there a way to get hg38 as reference? Or is there another way for me to call SNPs in Galaxy?

Thanks, Mei
snp • 772 views
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modified 2.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.3 years ago by Mei_Wu • 0
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gravatar for Jennifer Hillman Jackson
2.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

You could obtain the version of this genome from the GATK source bundle and use it as a custom reference genome.

I should let you know that using such a large custom genome with GATK tools at http://usegalaxy.org will likely create jobs that are too large to complete.

Also, the GATK version at this public site is older and the wrapper deprecated - meaning, they may not include all of the best practice tools you wish to use, may fail for odd reasons that will not be fixed, and the like.

The other option is to start up a local or cloud Galaxy, install the tools, install the reference genome, create indexes, and proceed.

Help:

Thanks, Jen, Galaxy team
ADD COMMENT • link modified 2.3 years ago • written 2.3 years ago by Jennifer Hillman Jackson ♦ 25k
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