Clinical-Genomics genmod issues

Clinical-Genomics / genmod

Annotate models of genetic inheritance patterns in variant files (vcf files)

http://moonso.github.io/genmod/

MIT License

71 stars 19 forks source link

issues

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Create VCF_DRSahajal

#129 DrParulGupta opened 3 months ago
1
Silently missing values when using integer format in rank model and encountering a float value

#128 Jakob37 opened 4 months ago
2
"Error: No such option: -f" message when running example

#127 hrydbeck opened 4 months ago
0
Phased models bugged?

#126 dnil opened 6 months ago
0
Unfreeze python version, fix collections import

#125 dnil opened 6 months ago
0
Makefile target for pypi dist upload

#124 torbjorgen opened 7 months ago
0
setup.py: Set version 3.8.2

#123 torbjorgen closed 7 months ago
0
Export Rankscore as Float Type

#122 torbjorgen closed 7 months ago
1
Mixed int-float in RankScore

#121 torbjorgen closed 7 months ago
0
setup.py: Lockdown genmod, limit compatibility to python v3.8

#120 torbjorgen closed 7 months ago
0
python3.10: import error

#119 jemten closed 7 months ago
1
setup.py: Set version 3.8.1

#118 torbjorgen closed 8 months ago
0
setup py uplift requirements

#117 torbjorgen closed 8 months ago
2
TypeError: annotate() got an unexpected keyword argument 'regions'

#116 manburst closed 7 months ago
2
container broken for version 3.8

#115 jemten closed 8 months ago
2
CHANGELOG, setup.py changes for v3.8.0

#114 torbjorgen closed 9 months ago
1
Tag, build new release

#113 torbjorgen closed 9 months ago
0
Link to documentation broken

#112 Jakob37 opened 9 months ago
1
set abstract_sockets_supported to False

#111 ramprasadn closed 10 months ago
1
Compound scoring: Cap rankscore values to (min, ) range

#110 torbjorgen closed 1 year ago
1
requirements: Set fixed version for deps

#109 torbjorgen closed 1 year ago
1
Rankscore normalization

#108 torbjorgen closed 9 months ago
11
Change or document AR_compound low scoring compound penalty

#107 dnil opened 1 year ago
0
Allow "Source" and "Version" in INFO header

#106 maehler opened 2 years ago
0
Error occurs if one or more variants in vep annotated VCF lacks VEP annotation when running with --vep

#105 bartcharbon opened 3 years ago
1
Use poetry as build tool

#104 moonso opened 3 years ago
0
Update docs on cli options

#103 moonso closed 3 years ago
0
parse new header format

#102 moonso closed 3 years ago
0
bug in parsing VCF header with filters that use escape character

#101 hassanfa closed 3 years ago
9
Documentation for "strict" and "phased" seems to be broken

#100 bartcharbon closed 3 years ago
1
Compound is missed if one parent is genotyped for each variant

#99 bartcharbon opened 3 years ago
4
Genmod models '--vep' option throws exception

#98 bartcharbon closed 3 years ago
6
Incorrect "Compounds" INFO field in case of multiallelic records

#97 bartcharbon closed 3 years ago
2
ANN standard format

#96 dridk opened 3 years ago
0
Implement a tier based ranking for somatic mutations

#95 hassanfa opened 4 years ago
2
no genetic model annotation

#94 caozongfu closed 4 years ago
0
Some variants without GeneticModels annotation

#93 geocarvalho closed 4 years ago
1
String matching in clinvar records..

#92 dnil opened 4 years ago
0
GenMod error: 'list' object has no attribute 'split'

#91 fgvieira closed 4 years ago
1
Incompatible CLI with click 7.0

#90 henrikstranneheim closed 5 years ago
0
Automatically determine pedigree?

#89 santiagorevale closed 5 years ago
1
No "GeneticModels=" in the output

#88 jielab closed 5 years ago
2
genmod score, data_type=string appears to match when the rule is a substring of the string in the VCF

#87 bjhall opened 6 years ago
0
"record_rule = max" appears to prioritize based on max(value) rather than max(score)

#86 bjhall opened 6 years ago
1
CSQ field is not parsed properly in genmod score when using --skip_plugin_check

#85 hassanfa opened 6 years ago
0
Food for thought: rank STR expansion variants?

#84 dnil closed 2 years ago
1
Fixes indentation error in genetic_models

#83 moonso closed 6 years ago
0
Compound error in 3.7.1 when single parent

#82 moonso closed 6 years ago
0
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