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Lrs pipeline updates#1115

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EddieLF wants to merge 11 commits intomainpopulationgenomics/production-pipelines:mainfrom lrs_pipeline_updatespopulationgenomics/production-pipelines:lrs_pipeline_updatesCopy head branch name to clipboard

+22-23

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Commits on Jan 17, 2025

• Update SV vcf query

  EddieLF

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  abf6889

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• Update SNV vcf query

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  8570045

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• Debug statements

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  87c6b99

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• Don't remove test

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  bb1fc10

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• Remove -test later on

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  6c8fcec

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• Remove more -test later on

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  6a651b7

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• Uppercase the sniffles allele

  EddieLF

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  7cebbed

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Commits on Jan 20, 2025

• Remove long_read flag from annotate_cohort job query command

  EddieLF

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  9fce003

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Commits on Jan 21, 2025

• Add a bcftools norm command before the merge vcfs stage

  EddieLF

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  8c6bedf

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• Update bcftools norm command with -N and add bcftools sort command

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  95cb9ec

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• Remove bcftools view, add bcftools norm options

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  05f5202

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