Commits · 1d0ab9e44db58fde2fa96b17798fe75159ae4a17 · igmmbioinformatics / trio-whole-exome

Feb 23, 2022
- Tools upgrade on bcbio · 1d0ab9e4
  ameyner2 authored 3 years ago
  
  1d0ab9e4
Dec 14, 2021
- Fix note on family 453955 · 77a56e8c
  ameyner2 authored 3 years ago
  
  77a56e8c
- Run notes for batch 19573 · 0f7e4ab8
  ameyner2 authored 3 years ago
  
  0f7e4ab8
- Fixed command typo · 7bf99fbb
  ameyner2 authored 3 years ago
  
  7bf99fbb
Nov 22, 2021
- LCR filtering. · d4b53c73
  ameyner2 authored 3 years ago
  
  d4b53c73
- Update SOP_alignment_variant_annotation.md · ecbed605
  ameyner2 authored 3 years ago
  
  ecbed605
Nov 19, 2021
- Update 19502_run_notes.md · e10de0f1
  ameyner2 authored 3 years ago
  
  e10de0f1
Nov 18, 2021
- Update tool_and_data_change_tracking.md · 6fc616ad
  mhalache authored 3 years ago
  
  6fc616ad
- Update tool_and_data_change_tracking.md · ad3d7df6
  ameyner2 authored 3 years ago
  
  ad3d7df6
- Update tool_and_data_change_tracking.md · 3a2520e2
  ameyner2 authored 3 years ago
  
  3a2520e2
- Update tool_and_data_change_tracking.md · 39a93ee5
  ameyner2 authored 3 years ago
  
  39a93ee5
- Tracks pipeline tool and data changes. · 5cdb7119
  ameyner2 authored 3 years ago
  
  5cdb7119
Nov 17, 2021
- Fix plot path · 3c4d841e
  ameyner2 authored 3 years ago
  
  3c4d841e
- Plots for strand bias investigation · 14f39d9d
  not populated not populated authored 3 years ago
  
  14f39d9d
- Initial investigation of strand bias metrics · dd4a3e4d
  ameyner2 authored 3 years ago
  
  dd4a3e4d
- Updated to include compression & md5 checksums (no archive required), and... · cf90a32a
  ameyner2 authored 3 years ago
  
  Updated to include compression & md5 checksums (no archive required), and added documentation around output file structure
  cf90a32a
- Fixed peddy parsing script for ultra2 · 419fd8d3
  ameyner2 authored 3 years ago
  
  419fd8d3
Nov 16, 2021
- Run notes for batch 19502 · d6e57bdf
  not populated not populated authored 3 years ago
  
  d6e57bdf
- First try at a CRF rapid run on ultra2 · 62f5abf3
  not populated not populated authored 3 years ago
  
  62f5abf3
Oct 04, 2021
- Added final params cleanup step · 5baf6371
  not populated not populated authored 3 years ago
  
  5baf6371
- Fixed relative path · dc19ab1f
  not populated not populated authored 3 years ago
  
  dc19ab1f
- Moved cram compression to Slurm, updated archiving SOP · 5c664b7e
  not populated not populated authored 3 years ago
  
  5c664b7e
- Added a cleanup step for bcbio config and param files · c331202b
  not populated not populated authored 3 years ago
  
  c331202b
- Renaming prepare bcbio config scripts for consistency · adde4a3c
  not populated not populated authored 3 years ago
  
  adde4a3c
- Use short project id for log files, move to prioritization next · ca876eab
  not populated not populated authored 3 years ago
  
  ca876eab
- Tidy up formatting · 5690f7f7
  not populated not populated authored 3 years ago
  
  5690f7f7
- MultiQC and PED check updated to ultra2 · f7cd78e2
  not populated not populated authored 3 years ago
  
  f7cd78e2
- _ultra2 docs moved to main copy · 1de6ebe9
  not populated not populated authored 3 years ago
  
  1de6ebe9
- _ultra2 docs moved to main copy · 7fe258a1
  not populated not populated authored 3 years ago
  
  7fe258a1
Sep 30, 2021
- First attempt at sbatch command for slurm system · 55e0eef2
  not populated not populated authored 3 years ago
  
  55e0eef2
Sep 29, 2021
- Project id then version and date for config generation logs, copy PED file... · fd4bc70d
  not populated not populated authored 3 years ago
  
  Project id then version and date for config generation logs, copy PED file rather than symbolic links
  fd4bc70d
- Fixed a few typos and clarified new output folder structure · b8b8d361
  not populated not populated authored 3 years ago
  
  b8b8d361
- Using Nextera read trimming for EdGe sequencing as well as CRF - only need a... · 48222543
  not populated not populated authored 3 years ago
  
  Using Nextera read trimming for EdGe sequencing as well as CRF - only need a single template & config file
  48222543
- Links rather than text copy for config files and bcbio templates · be512736
  not populated not populated authored 3 years ago
  
  be512736
Sep 07, 2021
- 19258 run notes · 06de3480
  ameyner2 authored 3 years ago
  
  06de3480
Aug 30, 2021
- Fix numbering · bdbf8ed2
  ameyner2 authored 3 years ago
  
  bdbf8ed2
- Initial draft of ultra2 SOP · 6fa150fb
  ameyner2 authored 3 years ago
  
  6fa150fb
- Ultra2 version of alignment & variant calling SOP · cb00f26e
  ameyner2 authored 3 years ago
  
  cb00f26e
Aug 26, 2021
- 19188 run notes first draft · d6b7860e
  ameyner2 authored 3 years ago
  
  d6b7860e
Aug 23, 2021
- Fixed a couple of resource paths · 15f1e1b2
  ameyner2 authored 3 years ago
  
  15f1e1b2