Gg foo #9279
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Gg foo #9279
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…emory or disk on certain task. (#8704)
…dSensitivity.wdl [VS-1245] (#8707)
* Remove AS_YNG from Extracted VCFs * Update test data to handle code change * Updated truth * Rebuild and update gatk docker.
…field from VCFs. (#8743)
ExtractCohortToPgen tool and workflow for running it based on the GVS VCF extract code Co-authored-by: Miguel Covarrubias <[email protected]>
* Update the reference disk lookup path.
* Had Hail Integration test tell VCF Integration test to ignore diffs in disk space or cost (which may be transient) * Added support for all_chrs truth. * Changed naming of cost and table sizes files to make replacement easier.
* Add new parameter to set filtered genotypes to no-calls to ExtractCohort * Modified ExtractCohortEngine to optionally set genotypes that are filtered (FT flag set - at the genotype leve) to no-calls. * Renamed VQSR Classic to 'VQSR' * Renamed VQSR Lite to 'VETS' * Updated VCF and pgen tests for code changes
* Fixed cost calculation to ignore duplicate rows caused by preemption. * Resetting tolerances to 5% across the board. We shall see.
* Optionally extract to bgz format. * Set bgzipping to be off (everywhere) by default. * Update assert_identical_outputs to handle bgzipped outputs.
* Have GvsAssignIds.wdl validate that input sample names (in the provided input file) are unique.
…ants tasks for FoxTrot Callset * Increase Default Disk for MergeVCFs task for FoxTrot Callset * Upping memory for SelectVariants for Foxtrot.
* VS-1716. Have Extract check for the existence of the sample_chromosome_ploidy table and use it if it exists. This should allow backwards compatibility with Delta callset.
…sites in a new location (#9255) * Update GvsCallsetStatistics.wdl to look for table gnomad_v3_sites in a new location.
* adding a testing WDL for VAT changes * adding a testing WDL for VAT changes * Adding in first pass at keeping the highest AC synonym and removing the rest * trying a different loop. Last one didn't work * Seeing if a string comparison instead of an integer comparison was behind the issue * Now with my debug info * Another round of better awking * piping synonyms to top-level test wdl * problem might be in awk version. Printing it * version of awk doesn't support --version?? * undoing version check * using some more verison-portable awk * Creating full VAT wdl to run against Echo data * Rounding up and saving the detailed list of lower ac synonyms that we filtered out * covering an edge case that we'll never actually see, but copilot pointed out. For completeness, I suppose * doing it as an inline python for loop * updating code to write the expected file instead of dumping to stdout * Removing helping wdl for efficient testing. Updating comments as per review feedback
* just do the query in two passes - even and odd numbered samples.
…somes (#9259) * Generalized the chromosome splitting.
* Add the variant id to the pgen output files
* Adding in check for contigs not in the weighed bed file so we no longer fail on that case * Pushing the changes to dockstore so I can check there instead of locally * updating GATK docker * Pointing us back to the normal weighted bed file instead of the interntionally broken one for testing
* Update VAT alt allele cutoff to 100 * Change logic for n_chunks to be echo-ish
* VS-1570 - Adding new validation for the VAT
* For VS-1644. Increase disk for ExcludeSitesFromSitesOnlyVcf task. Making it a task parameter so potentially overrideable.
* VS-1743. Modify pgen .pvar file to use a new ID field format. Specifically, 'chr:pos:ref'
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