moved EH to site-level #7178
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moved EH to site-level #7178
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kcibul
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kcibul
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…lts between WARP and BQ (#7179) * first pass * fixed to suppoer 1/0 1|0 genotypes * updates * updated workflow id * qualapprox updates from mmt branch (#7130) * handle multi-allelics and clean up diff output * updated alt allele script * excluding indels * updated for 37 sample tieout * full e2e tieout * formatting * output model/rscripts * Add model inputs to ngs_filter_extract (#7163) * add to dockstore.yml * add optional model inputs to ngs_filter_extract.wdl * add model input to indels VariantRecalibrator command * add missing model_report variable * fix indentation in .dockstore.yml * simplify model arguments * doc updates, tsv updates, fixed WARP dependencies to output model/RScript * modified parameters to use WARP excess het * doc updates * AH- add excess het (approx) to feature extract (#7175) * add approximate excess het calculation to feature extract and filter on it * added hacked version of XL * doc updates * moved EH to site-level (#7178) * cleanup of old VQSR feature input tieout * PR comments * PR comments Co-authored-by: M. Morgan Taylor <marymorg@broadinstitute.org> Co-authored-by: Andrea Haessly <ahaessly@broadinstitute.org>
mmorgantaylor
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Apr 6, 2021
…lts between WARP and BQ (#7179) * first pass * fixed to suppoer 1/0 1|0 genotypes * updates * updated workflow id * qualapprox updates from mmt branch (#7130) * handle multi-allelics and clean up diff output * updated alt allele script * excluding indels * updated for 37 sample tieout * full e2e tieout * formatting * output model/rscripts * Add model inputs to ngs_filter_extract (#7163) * add to dockstore.yml * add optional model inputs to ngs_filter_extract.wdl * add model input to indels VariantRecalibrator command * add missing model_report variable * fix indentation in .dockstore.yml * simplify model arguments * doc updates, tsv updates, fixed WARP dependencies to output model/RScript * modified parameters to use WARP excess het * doc updates * AH- add excess het (approx) to feature extract (#7175) * add approximate excess het calculation to feature extract and filter on it * added hacked version of XL * doc updates * moved EH to site-level (#7178) * cleanup of old VQSR feature input tieout * PR comments * PR comments Co-authored-by: M. Morgan Taylor <marymorg@broadinstitute.org> Co-authored-by: Andrea Haessly <ahaessly@broadinstitute.org>
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