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Module/gatk rnaseq/1.0#184

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Jwong684 wants to merge 18 commits intomasterLCR-BCCRC/lcr-modules:masterfrom module/gatk_rnaseq/1.0LCR-BCCRC/lcr-modules:module/gatk_rnaseq/1.0Copy head branch name to clipboard

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Commits on Apr 23, 2021

• Add initial draft of gatk_rnaseq version 1.0

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  e8874a5

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Commits on Apr 28, 2021

• Split gatk variant calling into per chromosome to speed up runs

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Commits on Apr 29, 2021

• Split up haplotype calling per chrom then merge

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Commits on May 5, 2021

• pulling from master

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  b760336

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• removed an outdated env yaml file

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  e2b4623

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Commits on May 6, 2021

• removes unnecessary lines

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• changelog updates

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Commits on May 7, 2021

• Documented changelog

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  cc95c65

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• Updated with new lcr-module checks

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Commits on May 9, 2021

• Updates to pull-request changes

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Commits on May 11, 2021

• Added a gnomad-filter step

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Commits on May 21, 2021

• added one line to config

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  1a11e3f

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Commits on May 31, 2021

• Added GATK_params as an extra param option for flexibility. Added and fixed a final gnomad-filtration step.

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Commits on Jul 22, 2021

• Added an RG rule before trimming

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Commits on Feb 18, 2022

• fixing commiting too many files

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  f422933

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• trying to merge master into branch

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  4acda94

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• updated the demo WGS bam links

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  f697c8f

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Commits on Apr 1, 2022

• Updated defaults and added AD and biallelic snp filtering step

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