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Question: HaplotypeCaller tool on galaxy
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gravatar for ib7
21 months ago by
ib7 • 0
United Kingdom
ib7 • 0 wrote:

is haplptypecaller form gatk avaialble on galaxy? icant seem to find it. There is UnifiedGenotyper, but the GATK website says "This tool has been deprecated in favor of HaplotypeCaller, a much more sophisticated variant caller that produces much better calls, especially on indels, and includes features that allow it to scale to much larger cohort sizes."

thanks ib7
galaxy gatk deprecated • 669 views
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modified 21 months ago by Jennifer Hillman Jackson ♦ 25k • written 21 months ago by ib7 • 0
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gravatar for vladimir.gritsenko
21 months ago by
vladimir.gritsenko • 90
Tel Aviv University
vladimir.gritsenko • 90 wrote:

Seems that GATK's license is too restrictive for Galaxy, so HaplotypeCaller won't be added in the foreseeable future. See Jennifer Jackson's answer and advice regarding alternative SNP callers here: https://biostar.usegalaxy.org/p/21564/#21616
ADD COMMENT • link written 21 months ago by vladimir.gritsenko • 90
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