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tgen
/
phoenix
Jetstream compatible workflow template supporting comprehensive analysis of human sequencing data against GRCh38
MIT License
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Potential for temp_dir to not exist during add_matched_rna
#473
bryce-turner
opened
1 year ago
0
Tumor Normal Filtering
#472
PedalheadPHX
opened
1 year ago
0
Update annotSeg_7102f1c.pl
#471
tizatt
opened
2 years ago
3
Initial mitochondrial somatic workflow
#470
fmadrid2
closed
4 months ago
0
Samtools markdup stats summary takes only one library
#469
denriquez
opened
2 years ago
0
Single cell updates
#468
bryce-turner
closed
2 years ago
1
Updates for UMI alignment workflow and gammit changes
#467
bryce-turner
closed
2 years ago
0
Gammit updates
#466
bryce-turner
closed
2 years ago
0
call consensus threads
#465
PedalheadPHX
opened
2 years ago
1
Second Metrics file for archive
#464
PedalheadPHX
opened
2 years ago
0
File for archive
#463
PedalheadPHX
opened
2 years ago
0
bwa-mem2
#462
PedalheadPHX
opened
2 years ago
0
Fulcrum umi
#461
bryce-turner
closed
2 years ago
1
GRCh38 difficult regions
#460
PedalheadPHX
opened
2 years ago
1
Update deepvariant to at least v1.0.0
#455
bryce-turner
opened
2 years ago
0
Wasted Compute
#454
PedalheadPHX
opened
3 years ago
0
Add IMGT VDJ reference to CellRanger Analysis
#453
ekelley903
opened
3 years ago
1
gatk_cnv step 3 has the potential of attempting to interpret log2 of 0
#452
bryce-turner
opened
3 years ago
0
Constitutional GATK CNV seg file in symbolic links
#451
PedalheadPHX
opened
3 years ago
3
GATK CNNscore produces empty VCF
#450
PedalheadPHX
opened
3 years ago
1
Release v1.2 versioning
#449
bryce-turner
closed
3 years ago
0
Update mutation_burden.jst
#448
bryce-turner
closed
3 years ago
0
GaMMiT reduction of frag_count in updated script
#447
bryce-turner
opened
3 years ago
1
release_v1.2
#446
bryce-turner
closed
3 years ago
1
Release v1.2 cleanup
#445
bryce-turner
closed
3 years ago
0
Bug fixes for sigprofiler and summarize_Ig
#444
bryce-turner
closed
3 years ago
0
Fixing sigprofiler output handling
#443
bryce-turner
closed
3 years ago
1
Fixing path naming for crai files
#442
bryce-turner
closed
3 years ago
0
The index files for md5sum bam/cram are also needed as input
#441
bryce-turner
closed
3 years ago
0
Bug fixes
#440
bryce-turner
closed
3 years ago
0
Bug fixes
#439
bryce-turner
closed
3 years ago
1
Feature: SigProfiler
#438
bryce-turner
closed
3 years ago
0
Feature: VCF Stats
#437
bryce-turner
closed
3 years ago
1
Updating fileType check for fasterq
#436
bryce-turner
closed
3 years ago
0
Feature: Constitutional gatk cnv
#435
bryce-turner
closed
3 years ago
0
Temp VCF Filtering
#434
bryce-turner
closed
3 years ago
0
Cellranger update
#433
bryce-turner
closed
3 years ago
1
HRD for BRCAness, measure the breaks within chromosome, less than an arm
#432
PedalheadPHX
closed
3 years ago
1
Feature: tHReD
#431
bryce-turner
closed
3 years ago
0
Feature: pcr free alignment
#430
bryce-turner
closed
3 years ago
2
Feature: Fasterq support
#429
bryce-turner
closed
3 years ago
0
Feature: Expansion hunter
#428
bryce-turner
closed
3 years ago
0
Annot seg bugfix
#427
bryce-turner
closed
3 years ago
0
mutation_burden format for stats2json and stats2lims
#426
bryce-turner
opened
3 years ago
0
Improper md5sum pathing
#425
bryce-turner
closed
3 years ago
0
VerifyBamID plotting script is hardcoded to use build 37
#423
bryce-turner
closed
3 years ago
1
KeyError: 'CCND1' at the end of Process_Assembled_BAM.py (trinity workflow)
#422
bryce-turner
closed
3 years ago
1
No Duplicate stats in LIMS for BAMs with multiple Libraries
#421
PedalheadPHX
opened
3 years ago
0
Resolves issue #418
#420
bryce-turner
closed
3 years ago
0
Question: CSI index on VCF
#419
PedalheadPHX
opened
3 years ago
0
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