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Question: Adding reference genome to Galaxy
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gravatar for tylertibetli
12 months ago by
tylertibetli • 0
tylertibetli • 0 wrote:

Hi, I want to add reference genome(hg19) from UCSC main table to my Galaxy account,how can I do that?I want to realign my reads and when I try to use GATK realigner,it asks reference genome.
alignment galaxy • 429 views
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modified 12 months ago • written 12 months ago by tylertibetli • 0
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gravatar for Jennifer Hillman Jackson
12 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The GATK tools hosted at https://usegalaxy.org are from a very old version (1.4) and have been deprecated for some time now. These are natively indexed for hg_g1k_v37 (1000 Genomes) and not hg19 (UCSC). Using hg19 from the history as a custom reference genome will cause several to fail for exceeding memory resources. We strongly recommend that you avoid using these tools.

Instead, please see the variant analysis tutorials here that include the most current tools and methods:

Thanks! Jen, Galaxy team
ADD COMMENT • link written 12 months ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for tylertibetli
12 months ago by
tylertibetli • 0
tylertibetli • 0 wrote:

Hi Jen,

Thank you for your assistance.
ADD COMMENT • link written 12 months ago by tylertibetli • 0
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