VAT cleanup and documentation #7531
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clean up annotations comment out ones that will be used in the future remove annotations I dont want
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rsasch
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Jan 3, 2022
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| ## make a file of just the first 5 columns of the tsv | ||
| ## During normalization, sometimes duplicate variamts appear but with different calculations. This seems to be a bug in bcftools. For now we arre dropping all duplicate variants | ||
| ## The say in which this is done is a bit hamfisted and should be optimized in the future. |
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nit: typo?
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| ## The say in which this is done is a bit hamfisted and should be optimized in the future. | |
| ## The way in which this is done is a bit hamfisted and should be optimized in the future. |
| @@ -326,9 +333,11 @@ task AnnotateVCF { | |||
| echo "Creating custom annotations" | |||
| mkdir customannotations_dir | |||
| CUSTOM_ANNOTATIONS_FOLDER="$PWD/customannotations_dir" | |||
| ## TODO this is a pass thru | |||
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This was referenced Mar 17, 2023
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Additional cleanup on the VAT--specifically focused on the failing shards and optimizing the workflow with them in mind.
As a next step, this workflow will be split up into 3 sub-workflows to keep the failures from knocking over the remaining likely-successful shards