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PEDIA-Charite
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PEDIA-workflow
PEDIA-workflow prioritizes the disease-causing gene by integrating facial analysis and exome sequencing data.
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hgvs-to-vcf does not work for some hgvs
#83
batsal
opened
2 years ago
0
Update VCF parser to support VCF format 4.3
#82
la60312
closed
4 years ago
0
Add phenomizer flag for disabling phenomizer in classification
#81
la60312
closed
4 years ago
0
Phenobot
#80
la60312
closed
4 years ago
0
Remove config.ini from repository
#79
la60312
opened
5 years ago
0
Update bcftools version
#78
la60312
opened
5 years ago
0
Skip updating config.yml when using -s
#77
la60312
opened
5 years ago
0
Enable running on unknown sample on server
#76
la60312
closed
5 years ago
0
Update errorfixer.py
#75
guyov1
closed
6 years ago
0
hgvs_erros.json contains non ascii character - fix by changing read command with "with open(path, mode="r", encoding='utf-8') as hgvs_file"
#74
guyov1
opened
6 years ago
0
Filter the variants not in exon
#73
la60312
opened
6 years ago
0
Support downloading via AWS and new qc
#72
la60312
closed
6 years ago
0
Resolves #70
#71
jakob-he
closed
6 years ago
2
Parsing error in genomic entry
#70
la60312
closed
6 years ago
0
Script for adding VCF to unsolved cases
#69
la60312
closed
6 years ago
0
Add new JSON format to QC pipeline
#68
jakob-he
opened
6 years ago
1
Convert check failed cases to old format
#67
la60312
closed
6 years ago
0
Twio errors while ignoring phenomizer and boqa
#66
la60312
closed
6 years ago
2
Add mas_mask in geneList
#65
la60312
closed
6 years ago
0
VCF conversion in server mode
#64
xiamaz
closed
6 years ago
6
Implementing Diagnosis Parsing and more QC stats
#63
xiamaz
closed
6 years ago
2
Caching
#62
xiamaz
closed
6 years ago
4
Implementing HGVS brackets parsing
#61
xiamaz
closed
6 years ago
0
Ability to run preprocess only on updated files
#60
xiamaz
closed
6 years ago
20
Remove config.yml from VCS
#59
xiamaz
closed
6 years ago
1
Only process new or updated cases
#58
la60312
opened
6 years ago
2
Always keep reference transcript in hgvs string formatting
#57
xiamaz
closed
6 years ago
0
Fixed config.yml generation
#56
jakob-he
closed
6 years ago
0
Implementing possibility to skip phenomizer
#55
xiamaz
closed
6 years ago
0
Fixing multi syndrome in check
#54
xiamaz
closed
6 years ago
0
Adding last_modified check in aws download
#53
xiamaz
closed
6 years ago
0
Log filtered empty cases
#52
la60312
closed
6 years ago
1
Apply manually fixed file to modify syndrome and gene
#51
la60312
closed
6 years ago
1
geneList merged on syndrome omim id
#50
xiamaz
closed
6 years ago
1
Correction of deprecated omim ids and fixed phenotypic series merging
#49
xiamaz
closed
6 years ago
0
case with selected syndrome with no omim_id were filtered out
#48
la60312
closed
6 years ago
0
Filter out the cases without features
#47
la60312
closed
6 years ago
1
resolves #45
#46
jakob-he
closed
6 years ago
0
Error in convert HGVS to VCF file
#45
la60312
closed
6 years ago
6
Remove redundant genomic data
#44
la60312
closed
6 years ago
0
Remove cases with multiple different disease causing gene
#43
la60312
closed
6 years ago
1
Add entrez id to genomicData
#42
la60312
closed
6 years ago
0
Fix missing and incorrect gene name
#41
la60312
closed
6 years ago
0
Lost converted gene entries from multiple different syndromes
#40
la60312
closed
6 years ago
2
Adding VCF checks to QC
#39
xiamaz
closed
6 years ago
0
Faster geneList generation by directly modifying dicts of dicts.
#38
xiamaz
closed
6 years ago
0
Snakemake dict does not work
#37
xiamaz
closed
6 years ago
0
No omim object. Some checks will not run.
#36
la60312
closed
6 years ago
8
strange behavior while generating VCF and config.yml
#35
la60312
closed
6 years ago
9
Fixing multi diagnosis detection
#34
xiamaz
closed
6 years ago
4
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