Code

Add DeepRVAT annotation pipeline#28

Code

Merged

endast merged 109 commits intomainPMBio/deeprvat:mainfrom deepripe-batchPMBio/deeprvat:deepripe-batchCopy head branch name to clipboardOct 20, 2023

+1,943-105

Commits

Commits on Aug 4, 2023

• added support for deepRiPe and deepSea, ability to concat and merge annotations into a single file

  

  “Marcel-Mueck”

  committed
  efd46a8

  Copy full SHA for efd46a8

• changed config file

  

  “Marcel-Mueck”

  committed
  1545c49

  Copy full SHA for 1545c49

• Create deeprvat_annotations.yml

  endast

  committed
  44702f9

  Copy full SHA for 44702f9

• Update deeprvat_annotations.yml

  Show description for a5fed75
  endast

  committed
  a5fed75

  Copy full SHA for a5fed75

• cleaned up commented out code in annotations.py

  

  “Marcel-Mueck”

  committed
  bb66bce

  Copy full SHA for bb66bce

• Merge branch 'Annotations' of github.com:PMBio/deeprvat into Annotations

  

  “Marcel-Mueck”

  committed
  f0e1b86

  Copy full SHA for f0e1b86

Commits on Aug 7, 2023

• Update deeprvat_annotations.yml

  Show description for 98aad4e
  endast

  committed
  98aad4e

  Copy full SHA for 98aad4e

• Update deeprvat_annotations.yml

  Show description for a012f2c
  endast

  committed
  a012f2c

  Copy full SHA for a012f2c

• Update deeprvat_annotations.yml

  Show description for b58f654
  endast

  committed
  b58f654

  Copy full SHA for b58f654

• Use python=3.9.16

  endast

  committed
  d6ef2f5

  Copy full SHA for d6ef2f5

• Update deeprvat_annotations.yml

  Show description for 74dd04e
  endast

  committed
  74dd04e

  Copy full SHA for 74dd04e

• increased memory resource for rule concat_deepSea

  

  “Marcel-Mueck”

  committed
  cfe68ca

  Copy full SHA for cfe68ca

• Merge branch 'main' into Annotations

  

  “Marcel-Mueck”

  committed
  deec6b7

  Copy full SHA for deec6b7

• Merge branch 'Annotations' of github.com:PMBio/deeprvat into Annotations

  

  “Marcel-Mueck”

  committed
  6e72396

  Copy full SHA for 6e72396

Commits on Aug 8, 2023

• Update deeprvat_annotations.yml

  Show description for 5091be0
  endast

  committed
  5091be0

  Copy full SHA for 5091be0

• deleted obsolete environment yaml file; removed absolute path from annotation config.

  

  “Marcel-Mueck”

  committed
  d8806e2

  Copy full SHA for d8806e2

• Merge branch 'Annotations' of github.com:PMBio/deeprvat into Annotations

  

  “Marcel-Mueck”

  committed
  b327392

  Copy full SHA for b327392

Commits on Aug 14, 2023

• updated environment, config, removed dask dependency

  

  “Marcel-Mueck”

  committed
  03218c8

  Copy full SHA for 03218c8

Commits on Aug 23, 2023

• changed annotations.py to make concatenation

  Show description for 3aac39a
  

  “Marcel-Mueck”

  committed
  3aac39a

  Copy full SHA for 3aac39a

Commits on Aug 24, 2023

• added support for different deepRIPE models (hg2, k5 and parclip)

  

  “Marcel-Mueck”

  committed
  c987400

  Copy full SHA for c987400

• fixup! Format Python code with psf/black pull_request

  

  PMBio

  authored and

  PMBio

  committed
  9a8391c

  Copy full SHA for 9a8391c

• changed some temporary paths

  

  “Marcel-Mueck”

  committed
  44acb9e

  Copy full SHA for 44acb9e

Commits on Aug 25, 2023

• filtering and aggregating vep columns

  

  “Marcel-Mueck”

  committed
  33a5b78

  Copy full SHA for 33a5b78

• fixup! Format Python code with psf/black pull_request

  

  PMBio

  authored and

  PMBio

  committed
  e18412c

  Copy full SHA for e18412c

• Update README.md

  Marcel-Mueck

  authored
  5d2c32c

  Copy full SHA for 5d2c32c

• Update README.md

  Marcel-Mueck

  authored
  5f9a2bc

  Copy full SHA for 5f9a2bc

• Update README.md

  Marcel-Mueck

  authored
  16206dc

  Copy full SHA for 16206dc

• Update README.md

  Marcel-Mueck

  authored
  f707b9e

  Copy full SHA for f707b9e

Commits on Sep 12, 2023

• speedups using joblib and batching

  bfclarke

  committed
  5d65cdf

  Copy full SHA for 5d65cdf

Commits on Sep 13, 2023

• remove unused function

  bfclarke

  committed
  1fec6f2

  Copy full SHA for 1fec6f2

Commits on Sep 14, 2023

• n_jobs as parameter

  

  “Marcel-Mueck”

  committed
  530da1f

  Copy full SHA for 530da1f

Commits on Sep 28, 2023

• Small changes

  

  “Marcel-Mueck”

  committed
  a85e404

  Copy full SHA for a85e404

• small changes

  

  “Marcel-Mueck”

  committed
  4be33e8

  Copy full SHA for 4be33e8

Commits on Oct 2, 2023

• elaborated data sources in README for annotations prescored data

  

  “Marcel-Mueck”

  committed
  1bff884

  Copy full SHA for 1bff884

Commits on Oct 5, 2023

• added required repos to requirements

  

  “Marcel-Mueck”

  committed
  c2ffb57

  Copy full SHA for c2ffb57

• clarified that user has to actiavte deeprvat_annotations

  

  “Marcel-Mueck”

  committed
  87a33ba

  Copy full SHA for 87a33ba

Commits on Oct 6, 2023

• added multithreading for deepripe scores to snakemake file

  

  “Marcel-Mueck”

  committed
  e91ca3d

  Copy full SHA for e91ca3d

• changed repo name

  

  “Marcel-Mueck”

  committed
  ebca4f0

  Copy full SHA for ebca4f0

• fixed input error on merge_deepripe rules

  

  “Marcel-Mueck”

  committed
  2d06c10

  Copy full SHA for 2d06c10

• added per-gene option in vep. no filtering to gene-variant pair level needed, added CONDEL score, changed pipeline to utilize more cores during runtime

  

  “Marcel-Mueck”

  committed
  a5125a8

  Copy full SHA for a5125a8

Commits on Oct 9, 2023

• added VEP plugin repo and faatpipe repo to config and setup.sh file

  

  “Marcel-Mueck”

  committed
  c3347c1

  Copy full SHA for c3347c1

• bug fix

  

  Clarke

  committed
  f3df8a8

  Copy full SHA for f3df8a8

Commits on Oct 11, 2023

• Update ensembl-vep version

  endast

  committed
  ae950cc

  Copy full SHA for ae950cc

Commits on Oct 13, 2023

• Make use of modules optional

  endast

  committed
  df20e1b

  Copy full SHA for df20e1b

• added merging of absplice ond deepsea pca to complete annotations in snakefile

  

  “Marcel-Mueck”

  committed
  2c62beb

  Copy full SHA for 2c62beb

• Merge branch 'deepripe-batch' of github.com:PMBio/deeprvat into deepripe-batch

  

  “Marcel-Mueck”

  committed
  138958b

  Copy full SHA for 138958b

• Fix processing of Uploaded_variation col

  endast

  committed
  11c69a5

  Copy full SHA for 11c69a5

• Merge branch 'deepripe-batch' of https://github.com/PMBio/deeprvat into deepripe-batch

  endast

  committed
  d9b303b

  Copy full SHA for d9b303b

• add vep to conda env

  endast

  committed
  81324a0

  Copy full SHA for 81324a0

• Merge branch 'deepripe-batch' of github.com:PMBio/deeprvat into deepripe-batch

  endast

  committed
  17580a3

  Copy full SHA for 17580a3

• Fix snakemake typos

  endast

  committed
  15f50bc

  Copy full SHA for 15f50bc

• Remoce unused import

  endast

  committed
  3bb17c6

  Copy full SHA for 3bb17c6

Commits on Oct 15, 2023

• Fix split of cols

  endast

  committed
  e29fcc0

  Copy full SHA for e29fcc0

• Only read the file in one place

  endast

  committed
  7be1915

  Copy full SHA for 7be1915

Commits on Oct 16, 2023

• fixed path names in snakemake rules

  

  “Marcel-Mueck”

  committed
  132efc4

  Copy full SHA for 132efc4

• Merge branch 'deepripe-batch' of github.com:PMBio/deeprvat into deepripe-batch

  Show description for 7cdb6ab
  

  “Marcel-Mueck”

  committed
  7cdb6ab

  Copy full SHA for 7cdb6ab

• small changes

  

  “Marcel-Mueck”

  committed
  22b979a

  Copy full SHA for 22b979a

• Use gz files

  endast

  committed
  5995e8b

  Copy full SHA for 5995e8b

• Update annotations.snakefile

  Show description for c9bb44b
  endast

  committed
  c9bb44b

  Copy full SHA for c9bb44b

Commits on Oct 17, 2023

• cast - as na in vep files

  endast

  committed
  c4b452c

  Copy full SHA for c4b452c

• pca object is saved and loaded as np array of components by default.

  

  “Marcel-Mueck”

  committed
  0599c89

  Copy full SHA for 0599c89

• Merge branch 'deepripe-batch' of github.com:PMBio/deeprvat into deepripe-batch

  

  “Marcel-Mueck”

  committed
  5affade

  Copy full SHA for 5affade

• Change vcf_file path to input_files

  endast

  committed
  1e0ab68

  Copy full SHA for 1e0ab68

Commits on Oct 18, 2023

• Update test data

  endast

  committed
  f1492b3

  Copy full SHA for f1492b3

• Fix columntypes

  endast

  committed
  3ff0ad1

  Copy full SHA for 3ff0ad1

• Merge branch 'deepripe-batch' of github.com:PMBio/deeprvat into deepripe-batch

  endast

  committed
  c8006a7

  Copy full SHA for c8006a7

• Fix typo in keyword argument

  endast

  committed
  e65e2c6

  Copy full SHA for e65e2c6

• Fix multiple merge problems from example run

  endast

  committed
  c7a21dc

  Copy full SHA for c7a21dc

• Merge branch 'main' into deepripe-batch

  endast

  committed
  66eb97c

  Copy full SHA for 66eb97c

• fixup! Format Python code with psf/black pull_request

  

  PMBio

  authored and

  PMBio

  committed
  c723aa0

  Copy full SHA for c723aa0

• Rename to pca_matrix

  endast

  committed
  0c45bf4

  Copy full SHA for 0c45bf4

• revert to components 100

  endast

  committed
  fb0f1e0

  Copy full SHA for fb0f1e0

Commits on Oct 19, 2023

• make deepsea_pca_n_components a config value

  endast

  committed
  a702e31

  Copy full SHA for a702e31

• add DeepRVAT-Annotation-Pipeline-Smoke-Tests

  endast

  committed
  d93b920

  Copy full SHA for d93b920

• rename bcf_file_pattern to source_variant_file_pattern

  endast

  committed
  ee0f3bc

  Copy full SHA for ee0f3bc

• Create pvcf_blocks.txt

  Show description for 8d1b0d5
  endast

  committed
  8d1b0d5

  Copy full SHA for 8d1b0d5

• Update github-actions.yml

  endast

  committed
  ff9d3d0

  Copy full SHA for ff9d3d0

• Add test vcf data

  endast

  committed
  5718952

  Copy full SHA for 5718952

• _variants_header is gzipped

  endast

  committed
  bb612b3

  Copy full SHA for bb612b3

• Fix extract variants

  endast

  committed
  b4ac7ca

  Copy full SHA for b4ac7ca

• Fix reference

  endast

  committed
  824b05e

  Copy full SHA for 824b05e

• Update github-actions.yml

  endast

  committed
  e983493

  Copy full SHA for e983493

• Create hg38.fa

  endast

  committed
  a9bb870

  Copy full SHA for a9bb870

• Update github-actions.yml

  endast

  committed
  0e0fdae

  Copy full SHA for 0e0fdae

• Create variants.tsv.gz

  endast

  committed
  d7d4f4f

  Copy full SHA for d7d4f4f

• Update github-actions.yml

  endast

  committed
  1a0680d

  Copy full SHA for 1a0680d

• Create .gitkeep

  endast

  committed
  bb0c60e

  Copy full SHA for bb0c60e

• Update github-actions.yml

  endast

  committed
  dced52f

  Copy full SHA for dced52f

• cleanup

  endast

  committed
  bac5dc1

  Copy full SHA for bac5dc1

• Revert "cleanup"

  Show description for 22a5442
  endast

  committed
  22a5442

  Copy full SHA for 22a5442

• Update github-actions.yml

  endast

  committed
  1ad2b25

  Copy full SHA for 1ad2b25

• Restore all pipelines

  endast

  committed
  2a444c6

  Copy full SHA for 2a444c6

• Cleanup

  endast

  committed
  c2b0226

  Copy full SHA for c2b0226

• Snakefmt annotations.snakefile

  endast

  committed
  51c7950

  Copy full SHA for 51c7950

Commits on Oct 20, 2023

• Update README.md

  Show description for fd2071c
  endast

  committed
  fd2071c

  Copy full SHA for fd2071c

• Refactor annotions.py

  endast

  committed
  9b04294

  Copy full SHA for 9b04294

• fixup! Format Python code with psf/black pull_request

  

  PMBio

  authored and

  PMBio

  committed
  510cc74

  Copy full SHA for 510cc74

• Refactor module load and add comments to conf

  endast

  committed
  528927a

  Copy full SHA for 528927a

• Merge branch 'deepripe-batch' of https://github.com/PMBio/deeprvat into deepripe-batch

  endast

  committed
  a2f19a1

  Copy full SHA for a2f19a1

• remove resources

  endast

  committed
  b3d22f1

  Copy full SHA for b3d22f1

• remove comment

  endast

  committed
  82e154d

  Copy full SHA for 82e154d

• remove comment

  endast

  committed
  be45635

  Copy full SHA for be45635

• add link to absplice readme

  endast

  committed
  fb58ed0

  Copy full SHA for fb58ed0

• add default chr

  endast

  committed
  c5be60d

  Copy full SHA for c5be60d

• snakefmt

  endast

  committed
  df354d6

  Copy full SHA for df354d6

• Use chr21,chr22 in example

  endast

  committed
  820a8a2

  Copy full SHA for 820a8a2

• Update annotations.snakefile

  endast

  committed
  5444ffd

  Copy full SHA for 5444ffd

• Fix load cmd from config

  endast

  committed
  569252b

  Copy full SHA for 569252b

• Update deeprvat_annotation_config.yaml

  endast

  committed
  5c4e2f4

  Copy full SHA for 5c4e2f4