VS-694 - Extract Callset for VQSR Lite #8182
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Minor changes to GvsCreateFilterSet.wdl and friends Create new ExtractCohortLite program for extraction of VQSR Lite data.
Make GvsExtractCallset.wdl run using VQSR Lite or VQSR Classic
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## ah_var_store #8182 +/- ##
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Coverage ? 85.857%
Complexity ? 35511
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Files ? 2194
Lines ? 167012
Branches ? 18001
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Hits ? 143392
Misses ? 17233
Partials ? 6387 |
…wdls. Update ExtractCohortLite to skip filtered records (temp fix)
mcovarr
approved these changes
Feb 8, 2023
…d to not load filtered sites into filter_set_info_vqsr_lite.
RoriCremer
reviewed
Feb 14, 2023
| @@ -15,8 +15,8 @@ workflow GvsCallsetStatistics { | |||
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| call Utils.ValidateFilterSetName { | |||
| input: | |||
| data_project = project_id, | |||
| dataset_name = dataset_name, | |||
| query_project = project_id, | |||
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are we going back to having the query proj being diff?
RoriCremer
reviewed
Feb 14, 2023
| # These calls to SelectVariants are being added for two reasons | ||
| # 1) The snps_variant_scored_vcf and indels_variant_scored_vcf output by JointVcfFiltering contains ALL variants, | ||
| # but are currently ONLY annotating SNPs and INDELs respectively. | ||
| # 2) Those output VCFs also contain filtered sites which we don't want to put into the filter_set_info_vqsr_lite table. |
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what does "filtered sites" here mean?
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Sites in the VCF that have the filter field set to anything other than '.' or 'PASS'.
This was referenced Mar 17, 2023
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Initial work on GvsExtractCallset.wdl
Minor changes to GvsCreateFilterSet.wdl and friends Create new ExtractCohortLite program for extraction of VQSR Lite data.