AH- add excess het (approx) to feature extract #7175
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kcibul
approved these changes
Mar 31, 2021
| builder.attribute("AS_MQRankSum", AS_MQRankSum==null?".":String.format("%.3f", AS_MQRankSum) ); | ||
| builder.attribute("AS_ReadPosRankSum", AS_ReadPosRankSum==null?".":String.format("%.3f", AS_ReadPosRankSum)); | ||
| builder.attribute("AS_SOR", String.format("%.3f", sor)); | ||
| builder.attribute(GATKVCFConstants.AS_QUAL_BY_DEPTH_KEY, String.format("%.2f", as_qd) ); |
| @@ -79,6 +79,8 @@ public static VCFFormatHeaderLine getEquivalentFormatHeaderLine(final String inf | |||
| addFilterLine(new VCFFilterHeaderLine(VQSR_TRANCHE_SNP, "Temporary VQSLOD cutoff for SNPs until we implememnt full tranche sensitivities")); | |||
| addFilterLine(new VCFFilterHeaderLine(VQSR_TRANCHE_INDEL, "Temporary VQSLOD cutoff for INDELs until we implememnt full tranche sensitivities")); | |||
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| addFilterLine(new VCFFilterHeaderLine(EXCESS_HET_KEY, "Site has excess het value larger than the threshold")); | |||
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I'm so surprised this wasn't there? How was WARP dealing with this?
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maybe it was just putting it in the INFO annotation and VQSR was doing the thresholding?
kcibul
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Apr 2, 2021
* add approximate excess het calculation to feature extract and filter on it
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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updated the query to calculate num hets and homvars
add in excess het and check threshold