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broadinstitute
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tgg_methods
Repo for miscellaneous methods developed by the methods group that don't fit anywhere else
MIT License
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gnomAD emails
#95
jialanm
closed
1 month ago
1
Run s&r checks on the 2 projects with the new pipeline
#94
jkgoodrich
closed
2 months ago
1
Add checks to generated tables (TPM, OUTRIDER, FRASER2) for seqr
#93
jialanm
opened
2 months ago
0
Generate sex and relatedness checks for old CMG projects
#92
jialanm
closed
2 months ago
0
Seqr Loading
#91
jialanm
closed
2 months ago
0
Lit review
#90
jkgoodrich
closed
2 months ago
0
PloidyConflict & Comprehensive Ploidy Investigation
#89
matren395
opened
2 months ago
1
Evaluate further returned GP/DSP quality metrics and GQ
#88
matren395
opened
2 months ago
3
Comprehensive sex & relatedness checks on DRAGEN/GVS callset
#87
matren395
opened
2 months ago
0
Implement new sex & relatedness checks for haploid-altered DRAGEN callsets
#86
matren395
opened
2 months ago
0
Pairwise investigation of GQ and other metrics between prior GATK/WARP RGP callset and RGP samples in DRAGEN-called GREGoR callset
#85
matren395
opened
2 months ago
3
Basic Sanity Check QC of DRAGEN-called GREGoR Callset
#84
matren395
closed
2 months ago
3
Implement changes to GVS-VETS into Seqr Loading Pipeline
#83
matren395
opened
2 months ago
0
Investigate and Resolve differences between DRAGEN/GVS and GATK/WARP seqr callsets
#82
jkgoodrich
opened
2 months ago
0
Add gnomAD small variant list query script
#81
jkgoodrich
closed
2 weeks ago
0
Update import_vcf.py with array_elements_required=False fix
#80
matren395
opened
7 months ago
0
Docker updates
#79
ch-kr
closed
10 months ago
0
Updated Hail in Dockerfile
#78
ch-kr
closed
10 months ago
0
modified tgps script
#77
jialanm
opened
11 months ago
1
Move VRS_VERSION constant definition
#76
matren395
closed
11 months ago
0
Update VRS Schema in vrs_annotation_batch.py
#72
matren395
closed
11 months ago
2
Create renaming/annotation script
#71
matren395
closed
1 year ago
0
Add Spark functionality as an option to VRS Annotation Script
#70
matren395
closed
1 year ago
0
Improve Performance by Removing/Modifying CloudFuse
#69
matren395
closed
1 year ago
0
v3.1.2 Release Table Duplication Big Fix (Temp)
#68
matren395
closed
1 year ago
0
Change to Check_Resource_Existence to update paths
#67
matren395
closed
1 year ago
0
Revise and Productionize Batch Script for VRS Annotation
#66
matren395
closed
1 year ago
2
Delete marten-temp-01-04_final-dataset-100k-01-04-23.vcf.bgz
#65
matren395
closed
1 year ago
0
Minor Dockerfile updates
#64
ch-kr
closed
1 year ago
0
Added Dataset Construction Script and Dataset
#63
matren395
closed
1 year ago
6
Create vrs subdirectory and vrs_readme_marten.txt
#62
matren395
closed
1 year ago
2
Add tmp_dir to init in subset.py
#61
ch-kr
closed
1 year ago
0
female->XX, male->XY
#60
mike-w-wilson
closed
1 year ago
1
Mw/sex check fix
#59
mike-w-wilson
closed
1 year ago
0
Update filters filter
#58
mike-w-wilson
closed
1 year ago
0
Remove outdated gcnv_viewer dir
#57
bw2
closed
1 year ago
1
Update gencode path and write OMIM table to file
#56
bw2
closed
1 year ago
0
Update assign_pops to work with gnomad update
#55
mike-w-wilson
opened
1 year ago
0
Update ensembl version
#54
bw2
opened
1 year ago
0
Fix bug that caused too large of sample lists per variant
#53
mike-w-wilson
closed
1 year ago
1
Script to find the number shared sites between pairs
#52
mike-w-wilson
closed
1 year ago
1
Bssp sex check
#51
DST310
closed
1 year ago
0
Demo PR #3
#50
ch-kr
closed
1 year ago
0
Demo PR #2
#49
ch-kr
closed
1 year ago
0
Demo PR
#48
ch-kr
closed
1 year ago
0
Mw/singletons
#47
mike-w-wilson
closed
1 year ago
1
Updated hail 0.2.93>0.2.95
#46
ch-kr
closed
2 years ago
2
Doubleton analysis
#45
ch-kr
closed
2 years ago
0
Wphu/add sex check
#44
williamphu
closed
1 year ago
0
Wphu/fix api calls
#43
williamphu
closed
2 years ago
2
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