Prioritizing non-coding variants#501

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dennishendriksen wants to merge 105 commits intomainfrom

feat/non-coding

Commits on Oct 10, 2022

Added custom VEP annotation for GREEN-DB constraint value.
JonathanKlimp
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Added the .bed.gz files containing the GREEN-DB constraint values
JonathanKlimp
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Changed Force report coordinates from 1 to 0
JonathanKlimp
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Fixed the quotes (") for the added custom GREEN-DB constraint command
JonathanKlimp
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added ../ to the input path for the GREEN-DB constraint command
JonathanKlimp
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Renamed and added the GREEN-DB constraint bed files for both build 38 as 38
JonathanKlimp
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Added path variable for the constraint .bed file to the pipeline
JonathanKlimp
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Revert "Renamed and added the GREEN-DB constraint bed files for both build 38 as 38"
JonathanKlimp
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update on the path variable to the green db constraint value file
JonathanKlimp
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renamed variable with GREEN-DB to GREEN_DB
JonathanKlimp
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added missing bracket
JonathanKlimp
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Commits on Oct 26, 2022

Edit on Fathmm_MKL custom argument variables
JonathanKlimp
committed

Commits on Oct 27, 2022

Update on nextflow.config. Changed fathmmMKL variable from .._fathmm_mkl_scores to .._fathmm_MKL_scores
JonathanKlimp
committed

Commits on Oct 28, 2022

added variables for ncER and ReMM tool scores
JonathanKlimp
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Commits on Nov 1, 2022

Commits on Nov 2, 2022

Uncommented fathmMKL for testing
JonathanKlimp
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Commits on Nov 10, 2022

added variable for HPO phenotype annotation
JonathanKlimp
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Commits on Nov 14, 2022

Commits on Nov 16, 2022

Added extra fathmm for the fathmm variable to let VEP know which values to use from the vcf
JonathanKlimp
committed

Commits on Nov 17, 2022

Commits on Nov 18, 2022

Commits on Nov 21, 2022

Commits on Nov 22, 2022

Commits on Dec 13, 2022

edited logging to file
JonathanKlimp
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Commits on Dec 14, 2022

Commits on Dec 20, 2022

Commits on Jan 25, 2023

changed ReMM from overlap to exact
JonathanKlimp
committed

Commits on Feb 3, 2023