Question: HaplotypeCaller tool on galaxy
0
gravatar for ib7
19 months ago by
ib70
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 gatk deprecated • 609 views
ADD COMMENTlink modified 19 months ago by Jennifer Hillman Jackson25k • written 19 months ago by ib70
1
gravatar for vladimir.gritsenko
19 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: https://biostar.usegalaxy.org/p/21564/#21616

ADD COMMENTlink written 19 months ago by vladimir.gritsenko90
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