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upgrade gvcf creation to gatk 4 eventually #35

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Kurt-Hetrick opened this issue Sep 10, 2018 · 2 comments
Open

upgrade gvcf creation to gatk 4 eventually #35

Kurt-Hetrick opened this issue Sep 10, 2018 · 2 comments
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enhancement New feature or request

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@Kurt-Hetrick
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I think the bug that has been found in the CF grant is actually occurring during GVCF creation (wasn't 100% clear to me that was the case, but it sounded like it). Also, I'm pretty sure that this is github issue for it.

broadinstitute/gatk#5171

the issue manifests as reference calls become missing.
@Kurt-Hetrick Kurt-Hetrick added the enhancement New feature or request label Sep 10, 2018
@Kurt-Hetrick
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looks like gatk 4.0.9.0 is a major improvement.

@Kurt-Hetrick
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this will take a lot of work to make it run somewhat expediently on local hpc...

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@Kurt-Hetrick