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OK we'll work with the recommendation to use HaplotypeCaller 4.0 unless we encounter other unexpected issues. I'd still be curious what was blocking Broad from using it in the production pipeline.
@Geraldine_VdAuwera @SChaluvadi Any thoughts?
@Schaluvadi I don't think that's the case (if it were, I'd already have over 10 points). Usually these systems give you points for doing different types of interaction, not the same one repeatedly. I think I got another point (up to 6 now) for lik…
I re-posted my actual question in the GATK forum since it belongs there. gatkforums.broadinstitute.org/gatk/discussion/13745/using-haplotypecaller-3-5-vs-haplotypecaller-4-0-joint-calling-large-cohorts/p1?new=1 (still can't link :( )
Meanwhile I'm seeing other people post questions about specific WDLs and referring to specific commits by link, this seems necessary. I've seen another thread where someone was "verified" so they could post links and this is what I want.
My question was referring to specific versions of GATK tools in specific WDLs published on github, and it's hard to be clear about versions and documentation without linking since there are many different scripts published in different repos. Here'…
@Sheila Thanks for your response. I have read the blog post you linked to, but my question is not straightforwardly addressed there. Let me re-phrase my question: Does the advice to omit IndelRealigner in HaplotypeCaller workflows apply to workfl…