Full scientific validation via end to end comparison of filtered results between WARP and BQ #7179
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* 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
* add approximate excess het calculation to feature extract and filter on it
.dockstore.yml
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| branches: | ||
| - master | ||
| - ah_var_store | ||
| - kc_feature_tieout |
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we can remove any references to branches other than master and ah_var_store (here and for cohort extract)
| bcftools view -O z SYNDIP.bq.all.vcf.gz chr20 > SYNDIP.bq.all.chr20.vcf.gz | ||
| tabix SYNDIP.bq.all.chr20.vcf.gz | ||
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| gsutil -m cp gvs.bq.all.vcf.gz* gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/warp/ |
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similar question as above - the NA12878 extraction uses gvs.bq.all.noeh.vcf.gz - i suspect this is just naming inconsistency?
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oops -- yeah naming consistency, I should have removed noeh
| First, create a full cohort extract (as described in README.md) using the `gvs_tieout_acmg_v3` (baseline), or otherwise desired, filtering model. | ||
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| ``` | ||
| ~/gatk SelectVariants -V gvs.bq.all.noeh.vcf.gz --sample-name SM-G947Y --select-type-to-exclude NO_VARIATION -O NA12878.bq.all.noeh.vcf.gz |
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per other threads - remove noeh here
| @@ -10,6 +10,7 @@ | |||
| import org.broadinstitute.hellbender.tools.variantdb.CommonCode; | |||
| import org.broadinstitute.hellbender.tools.variantdb.SampleList; | |||
| import org.broadinstitute.hellbender.tools.variantdb.SchemaUtils; | |||
| import org.broadinstitute.hellbender.utils.bigquery.BigQueryUtils; | |||
| ## RESEARCH: How to create list of excess het sites from WARP | ||
| ``` | ||
| rm excess_het_sites.bed | ||
| WORKFLOW_ID="c3733f56-218d-4242-af11-6557f101c5e2" |
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update for the good set:
WORKFLOW_ID="36e7547e-3253-4888-9b1c-2a7437401aee"
for f in `gsutil ls gs://broad-dsp-spec-ops-cromwell-execution/JointGenotyping/${WORKFLOW_ID}/call-HardFilterAndMakeSitesOnlyVcf/shard-*/*.sites_only.variant_filtered.vcf.gz `; do
echo "Processing $f"
gsutil cat $f | gunzip | awk '{ if ($7 == "ExcessHet") print $1"\t"($2-1)"\t"$2}' >> excess_het_sites.bed
done
mmorgantaylor
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Apr 2, 2021
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>
This was referenced Mar 17, 2023
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