testing something, please ignore #8251
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…r re-scattered shards (#7493)
* add param to just print final query * update print message
…tractCallset [VS-209] (#7495)
* export VAT to TSV * call export vat task * adding array values * pass the normalized vcf * clean up date spacing * loop through vms rather than in the task * remove partitioning because we are not going to do it for now
This reverts commit e6a9f77.
* add filtering on the FT tag level * remove duplicates by 4 cols, not only 2 * make annotations machine bigger * add duplicate count info * dont rename things---use the names that already exist! * drop all the excessive AS_QUALapprox info since it just adds weight * swap gzip * check with Lee about VAT - markings * template update * add in line counts for metrics * get the count of high alt allele sites * AC_hemi for all * add new docker image * get sample counts * clean up files for memory preservation * re-order errors * pass dropped variants * comments cleanup
* removed streaming * removed streaming * support for indexes as input * move to same directory * move to same directory * move to same directory part two * comments * comments * comments
* First implementation of working Reference Ranges-based Extract! * added integration test * PR cleanup * parameter cleanup * fix for upstream deletions * comments from PR * updated post rebase * cherry pick * Set gcloud config directory in travis (#7525) * Set gcloud config directory in travis * This fixes an issue while installing gcloud on travis due to permissions in the root directories Co-authored-by: Louis Bergelson <[email protected]>
* fix bug copying files * expose branch
* add reblocking wdl * rename wdl * make serivce account and site_id optional * add requester pays option * fix basename * change all outputs to file
* fix variable assignment
* change outputs to external bucket path
* use pending BQ writer * finalize stream before commit * update create tables for ref ranges * fix flushing and closing * use python to update data model * return error if response is not 200 * add bq table creation to assign ids, cleanup * update import with ref_ranges as default and 40 as drop state. update docs * fix tables for duplicate check * create separate readme for AoU Gvs workspace * handle null vet and pet creator * add initial test for write api * added sample_load_status table creation * log load status and verify sample is not loaded * used _default stream instead (#7588) * safety checks for restarts via preemptibles (#7590) * add is_loaded check back to GvsCreateFilterSet * 3 retries and bigger machine for writeAPI ingest (#7592)
* Renaming everything to use 'dataset_name'
* Added a new suite of tools for variant filtering based on site-level annotations. (#7954) * Adds wdl that tests joint VCF filtering tools (#7932) * adding filtering wdl * renaming pipeline * addressing comments * added bash * renaming json * adding glob to extract for extra files * changing dollar signs * small comments * Added changes for specifying model backend and other tweaks to WDLs and environment. * Added classes for representing a collection of labeled variant annotations. * Added interfaces for modeling and scoring backends. * Added a new suite of tools for variant filtering based on site-level annotations. * Added integration tests. * Added test resources and expected results. * Miscellaneous changes. * Removed non-ASCII characters. * Added documentation for TrainVariantAnnotationsModel and addressed review comments. Co-authored-by: meganshand <[email protected]> * Added toggle for selecting resource-matching strategies and miscellaneous minor fixes to new annotation-based filtering tools. (#8049) * Adding use_allele_specific_annotation arg and fixing task with empty input in JointVcfFiltering WDL (#8027) * Small changes to JointVCFFiltering WDL * making default for use_allele_specific_annotations * addressing comments * first stab * wire through WDL changes * fixed typo * set model_backend input value * add gatk_override to JointVcfFiltering call * typo in indel_annotations * make model_backend optional * tabs and spaces * make all model_backends optional * use gatk 4.3.0 * no point in changing the table names as this is a POC * adding new branch to dockstore * adding in branching logic for classic VQSR vs VQSR-Lite * implementing the separate schemas for the VQSR vs VQSR-Lite branches, including Java changes necessary to produce the different tsv files * passing classic flag to indel run of CreateFilteringFiles * Update GvsCreateFilterSet.wdl cleaning up verbiage * Removed mapping error rate from estimate of denoised copy ratios output by gCNV and updated sklearn. (#7261) * cleanup up sloppy comment --------- Co-authored-by: samuelklee <[email protected]> Co-authored-by: meganshand <[email protected]> Co-authored-by: Rebecca Asch <[email protected]>
* update deliverables to includes VDS notes * add some notes about default behavior * rip out VCF AoU instructions * tidy up useability * update comment on defaults * Update scripts/variantstore/docs/aou/AOU_DELIVERABLES.md Co-authored-by: Bec Asch <[email protected]> * Update scripts/variantstore/docs/aou/AOU_DELIVERABLES.md Co-authored-by: Bec Asch <[email protected]> * Update scripts/variantstore/docs/aou/AOU_DELIVERABLES.md Co-authored-by: Miguel Covarrubias <[email protected]> * update comments on python code * put correct script location in * fix markdown * add filter input to avro creation * cost notes * fix nits * add extract for control samples * add sts instructions * Update scripts/variantstore/docs/aou/AOU_DELIVERABLES.md Co-authored-by: Bec Asch <[email protected]> --------- Co-authored-by: Bec Asch <[email protected]> Co-authored-by: Miguel Covarrubias <[email protected]>
* limiting scatter width for beta customers in order to stay under google quotas * Just moving the beta scatter width to an argument so we can experiment with different numbers (if quotas are increased for a customer) without having to modify our code * renaming beta variable to something clearer then rearranging logic to unify the beta and broad use cases better.
…into beta workflow (#8200) * limiting scatter width for beta customers in order to stay under google quotas * Just moving the beta scatter width to an argument so we can experiment with different numbers (if quotas are increased for a customer) without having to modify our code * Piping beta information down to GvsImportGenomes * renaming beta variable to something clearer then rearranging logic to unify the beta and broad use cases better. * renaming beta variable * temporarily add it to dockstore * updating to a newer gatk * CromwellOnAzure + Azure SQL DB + AAD first steps doc [VS-805] (#8191) * bits of cleanup * Don't know why this got yanked in when I rebased * haste makes waste! --------- Co-authored-by: Miguel Covarrubias <[email protected]>
Update GvsExtractCallset to support VQSR Lite * Create new ExtractCohortLite program for extraction of VQSR Lite data. * Update dockers * Make GvsExtractCallset.wdl run using VQSR Lite or VQSR Classic * Name vqsr lite version of filter_set_info table consistently between wdls. * Update GvsCreateFilterSet.wdl to handle error in JointVcfFiltering and to not load filtered sites into filter_set_info_vqsr_lite.
* updating docker images * updating docker images... further * updating docker images to one that's actually correct * FOUND THE LAST ONE * Testing filter creation with George's docker image * dockstore * cleaning up docker
* VS-815: Add Support for YNG to VQSR Lite * Up the memory of a task in JointVcfFiltering.wdl. * Use 'HDD' rather than 'LOCAL' in JointVcfFiltering.wdl
* Update GvsCalculatePrecisionAndSensitivity.wdl to allow for different scale of calibration_sensitivity vs. lod score. Also retrieving score from JointVcfFiltering and storing that in BQ and in the VCF.
* deleted VDS * only one left
…tion of Delta (#8205) * Lees name * add vds validation script written by Tim * fix rd tim typo * make sure temp dir is set and not default for validate() * swap to consistent kebab case Co-authored-by: Miguel Covarrubias <[email protected]> * clean up validation * put init in the right place * add proper example to notes * update code formatting --------- Co-authored-by: Miguel Covarrubias <[email protected]>
* Lees name * add vds validation script written by Tim * fix rd tim typo * make sure temp dir is set and not default for validate() * swap to consistent kebab case Co-authored-by: Miguel Covarrubias <[email protected]> * clean up validation * put init in the right place * add proper example to notes * update code formatting * update review --------- Co-authored-by: Miguel Covarrubias <[email protected]>
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maxRetriesparameterized, default increased [VS-383] (LoadDatamaxRetriesparameterized, default increased [VS-383] #7791)