VAT Readme updates #8090
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VAT Readme updates #8090
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RoriCremer
commented
Nov 10, 2022
RoriCremer
commented
Nov 10, 2022
mcovarr
reviewed
Nov 10, 2022
| The third input is the ancestry file from the ancestry pipeline which will be used to calculate AC, AN and AF for all subpopulations. It needs to be copied into a GCP bucket that this pipeline will have access to. This input has been labelled as the `ancestry_file`. | ||
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| Most of the other files are specific to where the VAT will live, like the project_id and dataset_name and the table_suffix which will name the VAT itself as vat_`table_suffix` as well as a GCP bucket location, the output_path, for the intermediary files and the VAT export in tsv form. | ||
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| All optional inputs are provided with default values. | ||
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| ### Preparing to run GvsCreateVATfromVDS: | ||
| Three inputs need to be created from the VDS. | ||
| The third input can be created using the ancestry pipeline which is in another workspace. |
| ### Preparing to run GvsCreateVATfromVDS: | ||
| Three inputs need to be created from the VDS. | ||
| The third input can be created using the ancestry pipeline which is in another workspace. | ||
| The first and second inputs can be creating using this python script:`scripts/variantstore/wdl/extract/hail_create_vat_inputs.py` |
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must this be a cluster or could this be done in a WDL after copying down the inputs?
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good question---might be worth asking George actually. I'm not sure which he did
mcovarr
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Github actions tests reported job failures from actions build 3624257957
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This was referenced Mar 17, 2023
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Update the VAT pipeline readme to know about the VDS inputs
This will need to further be edited once George's VDS VAT pipeline changes have been completed