Question: HaplotypeCaller tool on galaxy
gravatar for ib7
13 months ago by
United Kingdom
ib70 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 • 406 views
ADD COMMENTlink modified 13 months ago by vladimir.gritsenko90 • written 13 months ago by ib70
gravatar for vladimir.gritsenko
13 months ago by
Tel Aviv University
vladimir.gritsenko90 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:

ADD COMMENTlink written 13 months ago by vladimir.gritsenko90
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