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Clinical-Genomics
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genmod
Annotate models of genetic inheritance patterns in variant files (vcf files)
http://moonso.github.io/genmod/
MIT License
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Adds functionality to use reference files with chr prefix. Fix #66
#81
moonso
closed
7 years ago
0
Handle empty files
#80
moonso
closed
7 years ago
0
Compund score key error
#79
moonso
closed
7 years ago
0
does not work
#78
brianlamx
closed
7 years ago
2
Add build 38
#77
moonso
closed
7 years ago
0
No constraint on lenght in contig headers. Fix #73
#76
moonso
closed
7 years ago
0
Fix contig pattern
#75
moonso
opened
7 years ago
0
genmod build command does not work
#74
brianlamx
closed
7 years ago
0
Fix SyntaxError due to missing contig length for multisample VCF generated by Freebayes
#73
nilesh-tawari
closed
7 years ago
1
Fix so that the program exits correct when there is a exception. Fix #53
#72
moonso
closed
7 years ago
1
Allow smaller queue to avoid memory problems for multiprocessing
#71
moonso
closed
7 years ago
0
Fix key error
#70
moonso
closed
7 years ago
0
Modify rank model for reduced penetrance genes
#69
henrikstranneheim
opened
7 years ago
0
Adds lacking csq information when scoring
#68
moonso
closed
7 years ago
0
vcf_extractor fails to find VEP format for CSQ score model?
#67
dnil
closed
7 years ago
2
Can not handle when chromosome prefix differs in vcf and resource
#66
moonso
closed
7 years ago
2
VEP Friendly Output
#65
AndrewSkelton
closed
7 years ago
2
Ped File
#64
AndrewSkelton
closed
8 years ago
5
Problem with encodings
#63
moonso
closed
8 years ago
0
handle about the GATKHardSNP in VCF header
#62
hmkim
closed
8 years ago
2
Add support for IMPRECISE variants when querying a ref vcf
#61
henrikstranneheim
opened
8 years ago
0
error with interval-tree
#60
mkohram
closed
7 years ago
5
Added option temp_dir. Fix #58
#59
moonso
closed
8 years ago
0
GENMOD on bigger VCF file - IO Error
#58
tinuthomas
closed
8 years ago
3
Handle no affected
#57
moonso
closed
8 years ago
0
Skip families without affected
#56
moonso
closed
8 years ago
0
GENMOD output gives pattern of inheritance for familes with no genotype data
#55
tinuthomas
closed
8 years ago
5
Genmod writes ExAC_MAX_AF to vcf header when using --thousand_g
#54
henrikstranneheim
closed
8 years ago
0
Catch error and make clean exit
#53
henrikstranneheim
closed
7 years ago
0
Fixed problem with sv alt fields. Added tests
#52
moonso
closed
8 years ago
0
Problem with SV alt fields
#51
moonso
closed
8 years ago
0
Add COSMIC annotation
#50
moonso
closed
8 years ago
0
Build Wiki
#49
AndrewSkelton
closed
8 years ago
4
Feature/compound problems
#48
moonso
closed
8 years ago
0
Problem with compounds when splitted with vt
#47
moonso
closed
8 years ago
0
installation issues ?
#46
parlar
closed
8 years ago
5
Add support to extract RS number, and MAX_AF from 1000G annotation as new info keys in vcf
#45
henrikstranneheim
closed
8 years ago
0
Add support for MT inheritance models
#44
henrikstranneheim
opened
8 years ago
3
Annotating with CADD Scores
#43
lukewbonham
closed
8 years ago
12
Problem with high GQ
#42
moonso
closed
8 years ago
0
Reducing AR_comp model noise
#41
dnil
closed
8 years ago
3
Modify geneticModels based on reduced penetrance for supplied genes
#40
henrikstranneheim
closed
8 years ago
3
New SO-terms
#39
moonso
closed
8 years ago
0
Problems with genmod score
#38
emmser
closed
8 years ago
0
Missing compounds
#37
robinandeer
closed
9 years ago
11
'generate_pairs' is not defined
#36
wclee47
closed
9 years ago
2
KeyError: u'genmod/configs/rank_model_test_v1.4.ini'
#35
wclee47
closed
9 years ago
5
Annotating with CADD
#34
landyk01
closed
9 years ago
4
Annotate with CADD not working
#33
landyk01
closed
9 years ago
1
Update build_annotation.py
#32
glabilloy
closed
9 years ago
1
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