Recreating Macrogen WES pipeline in Galaxy

usegalaxy.org support
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macrogen pipeline
macrogen pipeline704×564 67 KB

Can anyone assist in recreating this here or designing a pipeline that would work? What did you use instead of the GATK toolkit?

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Hi @Akili_Joseph, try FreeBayes for variant calling. Check GTN tutorials Galaxy Training!
Hope this helps.
Kind regards,
Igor