tjbencomo ngs-pipeline issues

tjbencomo / ngs-pipeline

Pipeline for Somatic Variant Calling with WES and WGS data

MIT License

20 stars 4 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

License lacking

#77 votti closed 4 months ago
2
Add somalier QC

#76 tjbencomo opened 2 years ago
0
See if cluster logs support wildcards in title

#75 tjbencomo closed 3 years ago
1
Re-examine WES resource allocations

#74 tjbencomo closed 3 years ago
0
Parallelize BQSR + Mutect2 PoN

#73 tjbencomo opened 3 years ago
0
V2.0

#72 tjbencomo closed 3 years ago
0
Update count_depths.py

#71 tjbencomo closed 3 years ago
0
Fix resources in cluster.wgs.json

#70 tjbencomo opened 3 years ago
0
Document behavior from split intervals with more than 24 workers

#69 tjbencomo closed 3 years ago
0
Update schema for latest fields

#68 tjbencomo closed 3 years ago
0
Major pipeline update

#67 tjbencomo closed 3 years ago
1
Switch to singularity containers completely

#66 tjbencomo closed 3 years ago
0
Add stringent variant filtering option

#65 tjbencomo closed 3 years ago
0
Make mutect2 vcf interval files temporary

#64 tjbencomo closed 3 years ago
0
Add cluster.json info for split_intervals rule

#63 tjbencomo closed 3 years ago
0
Create separate cluster.json files for exome vs whole genome

#62 tjbencomo closed 3 years ago
0
Keep filtering stats file

#61 tjbencomo closed 3 years ago
0
Add cluster specs for merge_vcfs, merge_stats, and orientation_bias

#60 tjbencomo closed 3 years ago
0
Parallelize BQSR and MarkDups + SortSam

#59 tjbencomo closed 3 years ago
1
Parallel mutect2

#58 tjbencomo closed 4 years ago
0
Remove --use-original-qualities from bqsr?

#57 tjbencomo closed 4 years ago
1
Tumor only

#56 tjbencomo closed 4 years ago
0
Add rules for plot-depths

#55 tjbencomo closed 4 years ago
0
Plot depth

#54 tjbencomo closed 4 years ago
0
Add script to calculate average depth for each sample

#53 tjbencomo closed 4 years ago
0
Add report generation

#52 tjbencomo opened 4 years ago
0
Annotation issues

#51 tjbencomo closed 4 years ago
0
Add Panel of Normals Creation Workflow

#50 tjbencomo closed 4 years ago
0
Add workflow to create Panel of Normals

#49 tjbencomo closed 4 years ago
1
Add logging to each rule

#48 tjbencomo closed 3 years ago
0
Sort units index before accessing indices to increase performance

#47 tjbencomo closed 4 years ago
0
Allow naming of either upper or lower case Normal/Tumor sample types

#46 tjbencomo opened 4 years ago
0
Multiplexed samples

#45 tjbencomo closed 4 years ago
0
Update Mutect2 Calling Workflow

#44 tjbencomo closed 4 years ago
1
Add more Variant Callers

#43 tjbencomo opened 4 years ago
0
Handle multiple FASTQs from different lanes for same sample

#42 tjbencomo closed 4 years ago
2
Change naming

#41 tjbencomo closed 4 years ago
0
Remove bqsr report from MultiQC inputs

#40 tjbencomo closed 4 years ago
0
Change naming conventions

#39 tjbencomo closed 4 years ago
0
Add ability for user to specify custom names for control and tumor types

#38 tjbencomo opened 4 years ago
0
Run BQSR twice to get pre and post calibration tables

#37 tjbencomo closed 4 years ago
1
V1.0.1

#36 tjbencomo closed 4 years ago
0
Add ability to handle custom read groups

#35 tjbencomo closed 4 years ago
1
Look into Snakemake not realizing SLURM job timed out

#34 tjbencomo opened 4 years ago
0
Implement changes from test run

#33 tjbencomo closed 4 years ago
2
Add section on singularity + Conda vs Conda alone

#32 tjbencomo closed 4 years ago
0
Add var annot

#31 tjbencomo closed 4 years ago
0
Add VCF consolidation into multi-sample file

#30 tjbencomo closed 4 years ago
1
Finished creating shrunk ref files for end-to-end testing. Added all …

#29 tjbencomo closed 4 years ago
0
Add bwa index step

#28 tjbencomo closed 4 years ago
0