VCF annotation using VEP - [merged]

[ManavalanG]

_Merges vepannotation -> master

Annotates variants in VCF using Variant Effect Predictor (VEP).

The following may need review at some level. Note this other stuff may need review as well, as this is not exhaustive.

• [x] Snakemake pipeline
• [x] Source code directory structure. It may be a good idea to spend some time on this so the repo with several moving parts will remain manageable.
• [x] Documentation. I kept it simple; let me know if it needs more info.
• [x] Datasets used and their versions

[ManavalanG]

 into a single file, bgzipped and indexed.

[ManavalanG]

In GitLab by @wilkb777 on Jan 29, 2021, 12:07

ok, the CLI has been added now so I'll resolve the thread.

[ManavalanG]

In GitLab by @wilkb777 on Jan 29, 2021, 12:08

Commented on variant_annotation/README.md line 47

changed this line in version 11 of the diff

[ManavalanG]

In GitLab by @wilkb777 on Jan 29, 2021, 12:08

added 1 commit

• a25bf724 - Apply 1 suggestion(s) to 1 file(s)

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[ManavalanG]

LG2M

[ManavalanG]

resolved all threads

[ManavalanG]

In GitLab by @wilkb777 on Jan 29, 2021, 12:24

marked the checklist item Documentation. I kept it simple; let me know if it needs more info. as completed

[ManavalanG]

In GitLab by @wilkb777 on Jan 29, 2021, 12:24

approved this merge request

[ManavalanG]

In GitLab by @wilkb777 on Jan 29, 2021, 12:24

marked this merge request as ready

[ManavalanG]

In GitLab by @wilkb777 on Jan 29, 2021, 12:27

added 1 commit

• 82a84ce1 - untracking unused file

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[ManavalanG]

In GitLab by @wilkb777 on Jan 29, 2021, 12:38

added 37 commits

• 96dd2599 - refactors snakefile to standardize a bit
• abde5561 - adds cluster config
• 0a3416be - adds snakemake slurm profile as git submodule
• 77e32c5d - adds snakemake slurm profile as submodule
• 4fc35d54 - removes pipeline specific logs
• 9a0de28f - updates snakemake command and resources
• 2696afdc - fixes filepaths
• ffabcee7 - fix to avoid conda env conflict
• 3188ac69 - bumps up ref version to use
• 2b16f73d - updates gnomad fields
• 0613055f - adds test vcf, thanks to Brandon
• b16b88e9 - updates clinvar fields
• 70b8b06d - changes case for readability
• f8a6c79f - annotations with dbnfsp
• d74d4f52 - adds more dbnsfp fields
• 0bd2f7a6 - changes to improve speed
• c67392bb - fiexes minor bug
• 6e29733c - cleans up dir structure and doc
• 274ba37e - updates doc
• 40539149 - adds annotated test vcf
• f107d640 - fixes resources config bug
• 635a5d18 - uses VEP's sift and polyphen; changes threads to 8
• f9714adb - adds warning file
• ddbc558d - breaks long strings to multi-lines
• dc2ad99d - bumps cluster partition; update test output
• de29e7bb - bgzips output vcf
• fb0d8906 - updates conda env
• ffdd6181 - refactors vep to directly write bgzipped output file
• dc79fdd1 - accepts input vcf via config
• ba9add15 - adds test output
• 6fae0ccf - inputs datasets config via cli
• 5bd9ab7c - downgrades cluster partition for annotation
• eb16285f - removes unused code
• c420c811 - making changes to add CLI specification of input info
• 4b354a7b - fixing stupid mistake in CLI arg check
• 92113ce0 - minor updates based on recommendations, added some dataset info to readme
• 78a485c7 - Apply 1 suggestion(s) to 1 file(s)

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[ManavalanG]

mentioned in commit 624418aacd5511fe718fa818f696c22f5e3dfe91