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Adding GATK concordance script (connected to #167) #173

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Adding GATK concordance script (connected to #167) #173

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heuermh
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@heuermh heuermh commented Mar 14, 2016

Work towards #167, still needs to be tested.

@heuermh heuermh changed the title first checked in Adding GATK concordance script Mar 14, 2016
@hannes-ucsc hannes-ucsc changed the title Adding GATK concordance script Adding GATK concordance script (resolves #167) Mar 14, 2016
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Fixed title and added needs work label. Let me know if any of these changes are inaccurate.

fnothaft
fnothaft reviewed Mar 14, 2016
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src/toil_scripts/gatk_concordance/gatk_concordance.py
return parser


# copied from germline.py
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NONONONONONONONONONONONONONONO! No copying!

:)

@fnothaft fnothaft changed the title Adding GATK concordance script (resolves #167) Adding GATK concordance script Mar 16, 2016
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I've removed the "Resolves #167" title, as we still need liftover code. @heuermh will you add VCF liftover to this, or open a new PR with it? I'd probably prefer a new PR.

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heuermh commented Mar 16, 2016

Sure, in a new PR

@hannes-ucsc hannes-ucsc changed the title Adding GATK concordance script Adding GATK concordance script (connected to #167) Mar 16, 2016
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In that case the connected to linkage is recommended. It's used by Waffle to stack PRs and issues.

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@heuermh @hannes-ucsc @fnothaft