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TODO: v1.0.0 Release #13
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Add support for WES data
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Germline Pipeline
This will prevent any unnecessary compute and will reduce overall runtime.
Fix strelka issue
Filtering from GATK is not working for strelka, resolved by adding these two commands before it goes to norm & splitting:
Next fix is for spliting TUMOR from strelka. When splitting we cannot use "-c1" for strelka as we don't have the tag in vcf file to check for
--min-ac/--max-ac
. We need to update the tumor splitting command for strelka to remove -c1:Tumor only
Need to update rule all so that the strelka and muse output files do not get created for tumor-only samples
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