bcftools to the rescue #7456
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bcftools to the rescue #7456
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rsasch
approved these changes
Sep 21, 2021
| WHERE | ||
| gvs_all_ac != gvs_afr_an + gvs_amr_an + gvs_eas_an + gvs_eur_an + gvs_mid_an + gvs_oth_an + gvs_sas_an' | ||
|
|
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| # if the result of the query has any rows, that means gvs_all_an has not been calulated correctly/ |
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nit
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| # if the result of the query has any rows, that means gvs_all_an has not been calulated correctly/ | |
| # if the result of the query has any rows, that means gvs_all_an has not been calculated correctly |
| # ------------------------------------------------ | ||
| # Output: {"Name of validation rule": "PASS/FAIL plus additional validation results"} | ||
| output { | ||
| Map[String, String] result = {"SubpopulationAlleleCount": read_string('validation_results.txt')} |
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| Map[String, String] result = {"SubpopulationAlleleCount": read_string('validation_results.txt')} | |
| Map[String, String] result = {"SubpopulationAlleleNumber": read_string('validation_results.txt')} |
This was referenced Mar 17, 2023
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Keeping the dockstore as is for now because I may want to run this on a few shards from the 30k while it's still in review
This pr adds a fair amount of work to the bcftools task (ExtractAnAcAfFromVCF) and adds a significant number of columns to the schema: the sample count for all of the samples, as well as for each subpopulation.
Note that AC_hemi will be added in a follow on pr
Note that additional validation tests will be added in a follow on pr