Clinical-Genomics/genmod issues and pull requests

#118 - setup.py: Set version 3.8.1

Pull Request - State: closed - Opened by torbjorgen 8 months ago

#117 - setup py uplift requirements

Pull Request - State: closed - Opened by torbjorgen 8 months ago - 2 comments

#116 - TypeError: annotate() got an unexpected keyword argument 'regions'

Issue - State: open - Opened by manburst 8 months ago

#115 - container broken for version 3.8

Issue - State: closed - Opened by jemten 8 months ago - 2 comments

#114 - CHANGELOG, setup.py changes for v3.8.0

Pull Request - State: closed - Opened by torbjorgen 9 months ago - 1 comment

#113 - Tag, build new release

Issue - State: closed - Opened by torbjorgen 9 months ago

#112 - Link to documentation broken

Issue - State: open - Opened by Jakob37 9 months ago

#111 - set abstract_sockets_supported to False

Pull Request - State: closed - Opened by ramprasadn 11 months ago - 1 comment

#110 - Compound scoring: Cap rankscore values to (min, ) range

Pull Request - State: closed - Opened by torbjorgen about 1 year ago - 1 comment

#109 - requirements: Set fixed version for deps

Pull Request - State: closed - Opened by torbjorgen about 1 year ago - 1 comment

#108 - Rankscore normalization

Pull Request - State: closed - Opened by torbjorgen about 1 year ago - 11 comments

#107 - Change or document AR_compound low scoring compound penalty

Issue - State: open - Opened by dnil over 1 year ago

#106 - Allow "Source" and "Version" in INFO header

Pull Request - State: open - Opened by maehler about 2 years ago

#105 - Error occurs if one or more variants in vep annotated VCF lacks VEP annotation when running with --vep

Issue - State: open - Opened by bartcharbon over 3 years ago - 1 comment

#104 - Use poetry as build tool

Pull Request - State: open - Opened by moonso over 3 years ago

#103 - Update docs on cli options

Pull Request - State: closed - Opened by moonso over 3 years ago

#102 - parse new header format

Pull Request - State: closed - Opened by moonso over 3 years ago

#101 - bug in parsing VCF header with filters that use escape character

Issue - State: closed - Opened by hassanfa over 3 years ago - 9 comments

#100 - Documentation for "strict" and "phased" seems to be broken

Issue - State: closed - Opened by bartcharbon over 3 years ago - 1 comment

#99 - Compound is missed if one parent is genotyped for each variant

Issue - State: open - Opened by bartcharbon over 3 years ago - 4 comments

#98 - Genmod models '--vep' option throws exception

Issue - State: closed - Opened by bartcharbon over 3 years ago - 6 comments

#97 - Incorrect "Compounds" INFO field in case of multiallelic records

Issue - State: closed - Opened by bartcharbon over 3 years ago - 2 comments

#96 - ANN standard format

Issue - State: open - Opened by dridk almost 4 years ago

#95 - Implement a tier based ranking for somatic mutations

Issue - State: open - Opened by hassanfa about 4 years ago - 2 comments

#94 - no genetic model annotation

Issue - State: closed - Opened by caozongfu about 4 years ago

#93 - Some variants without GeneticModels annotation

Issue - State: closed - Opened by geocarvalho over 4 years ago - 1 comment

#92 - String matching in clinvar records..

Issue - State: open - Opened by dnil over 4 years ago

#91 - GenMod error: 'list' object has no attribute 'split'

Issue - State: closed - Opened by fgvieira almost 5 years ago - 1 comment

#90 - Incompatible CLI with click 7.0

Issue - State: closed - Opened by henrikstranneheim over 5 years ago
Labels: bug

#89 - Automatically determine pedigree?

Issue - State: closed - Opened by santiagorevale almost 6 years ago - 1 comment

#88 - No "GeneticModels=" in the output

Issue - State: closed - Opened by jielab almost 6 years ago - 2 comments

#87 - genmod score, data_type=string appears to match when the rule is a substring of the string in the VCF

Issue - State: open - Opened by bjhall about 6 years ago

#86 - "record_rule = max" appears to prioritize based on max(value) rather than max(score)

Issue - State: open - Opened by bjhall about 6 years ago - 1 comment

#85 - CSQ field is not parsed properly in genmod score when using --skip_plugin_check

Issue - State: open - Opened by hassanfa about 6 years ago

#84 - Food for thought: rank STR expansion variants?

Issue - State: closed - Opened by dnil over 6 years ago - 1 comment

#83 - Fixes indentation error in genetic_models

Pull Request - State: closed - Opened by moonso almost 7 years ago

#82 - Compound error in 3.7.1 when single parent

Issue - State: closed - Opened by moonso almost 7 years ago

#81 - Adds functionality to use reference files with chr prefix. Fix #66

Pull Request - State: closed - Opened by moonso over 7 years ago

#80 - Handle empty files

Pull Request - State: closed - Opened by moonso over 7 years ago

#79 - Compund score key error

Pull Request - State: closed - Opened by moonso over 7 years ago

#78 - does not work

Issue - State: closed - Opened by brianlamx over 7 years ago - 2 comments

#77 - Add build 38

Pull Request - State: closed - Opened by moonso over 7 years ago

#76 - No constraint on lenght in contig headers. Fix #73

Pull Request - State: closed - Opened by moonso over 7 years ago

#75 - Fix contig pattern

Pull Request - State: open - Opened by moonso over 7 years ago

#74 - genmod build command does not work

Issue - State: closed - Opened by brianlamx over 7 years ago

#73 - Fix SyntaxError due to missing contig length for multisample VCF generated by Freebayes

Issue - State: closed - Opened by nilesh-tawari over 7 years ago - 1 comment
Labels: enhancement

#72 - Fix so that the program exits correct when there is a exception. Fix #53

Pull Request - State: closed - Opened by moonso over 7 years ago - 1 comment

#71 - Allow smaller queue to avoid memory problems for multiprocessing

Pull Request - State: closed - Opened by moonso over 7 years ago

#70 - Fix key error

Pull Request - State: closed - Opened by moonso over 7 years ago

#69 - Modify rank model for reduced penetrance genes

Issue - State: open - Opened by henrikstranneheim over 7 years ago

#68 - Adds lacking csq information when scoring

Pull Request - State: closed - Opened by moonso over 7 years ago

#67 - vcf_extractor fails to find VEP format for CSQ score model?

Issue - State: closed - Opened by dnil almost 8 years ago - 2 comments

#66 - Can not handle when chromosome prefix differs in vcf and resource

Issue - State: closed - Opened by moonso almost 8 years ago - 2 comments

#65 - VEP Friendly Output

Issue - State: closed - Opened by AndrewSkelton about 8 years ago - 2 comments

#64 - Ped File

Issue - State: closed - Opened by AndrewSkelton about 8 years ago - 5 comments

#63 - Problem with encodings

Issue - State: closed - Opened by moonso about 8 years ago

#62 - handle about the GATKHardSNP in VCF header

Issue - State: closed - Opened by hmkim about 8 years ago - 2 comments

#61 - Add support for IMPRECISE variants when querying a ref vcf

Issue - State: open - Opened by henrikstranneheim about 8 years ago
Labels: enhancement

#60 - error with interval-tree

Issue - State: closed - Opened by mkohram about 8 years ago - 5 comments

#59 - Added option temp_dir. Fix #58

Pull Request - State: closed - Opened by moonso about 8 years ago

#58 - GENMOD on bigger VCF file - IO Error

Issue - State: closed - Opened by tinuthomas about 8 years ago - 3 comments

#57 - Handle no affected

Pull Request - State: closed - Opened by moonso about 8 years ago

#56 - Skip families without affected

Issue - State: closed - Opened by moonso about 8 years ago

#55 - GENMOD output gives pattern of inheritance for familes with no genotype data

Issue - State: closed - Opened by tinuthomas about 8 years ago - 5 comments

#54 - Genmod writes ExAC_MAX_AF to vcf header when using --thousand_g

Issue - State: closed - Opened by henrikstranneheim about 8 years ago

#53 - Catch error and make clean exit

Issue - State: closed - Opened by henrikstranneheim over 8 years ago

#52 - Fixed problem with sv alt fields. Added tests

Pull Request - State: closed - Opened by moonso over 8 years ago

#51 - Problem with SV alt fields

Issue - State: closed - Opened by moonso over 8 years ago

#50 - Add COSMIC annotation

Issue - State: closed - Opened by moonso over 8 years ago

#49 - Build Wiki

Issue - State: closed - Opened by AndrewSkelton over 8 years ago - 4 comments

#48 - Feature/compound problems

Pull Request - State: closed - Opened by moonso over 8 years ago

#47 - Problem with compounds when splitted with vt

Issue - State: closed - Opened by moonso over 8 years ago

#46 - installation issues ?

Issue - State: closed - Opened by parlar over 8 years ago - 5 comments

#45 - Add support to extract RS number, and MAX_AF from 1000G annotation as new info keys in vcf

Issue - State: closed - Opened by henrikstranneheim over 8 years ago

#44 - Add support for MT inheritance models

Issue - State: open - Opened by henrikstranneheim over 8 years ago - 3 comments

#43 - Annotating with CADD Scores

Issue - State: closed - Opened by lukewbonham over 8 years ago - 12 comments

#42 - Problem with high GQ

Issue - State: closed - Opened by moonso almost 9 years ago

#41 - Reducing AR_comp model noise

Issue - State: closed - Opened by dnil almost 9 years ago - 3 comments

#40 - Modify geneticModels based on reduced penetrance for supplied genes

Issue - State: closed - Opened by henrikstranneheim almost 9 years ago - 3 comments

#39 - New SO-terms

Issue - State: closed - Opened by moonso almost 9 years ago

#38 - Problems with genmod score

Issue - State: closed - Opened by emmser about 9 years ago

#37 - Missing compounds

Issue - State: closed - Opened by robinandeer about 9 years ago - 11 comments

#36 - 'generate_pairs' is not defined

Issue - State: closed - Opened by wclee47 about 9 years ago - 2 comments

#35 - KeyError: u'genmod/configs/rank_model_test_v1.4.ini'

Issue - State: closed - Opened by wclee47 about 9 years ago - 5 comments

#34 - Annotating with CADD

Issue - State: closed - Opened by landyk01 over 9 years ago - 4 comments

#33 - Annotate with CADD not working

Issue - State: closed - Opened by landyk01 over 9 years ago - 1 comment

#32 - Update build_annotation.py

Pull Request - State: closed - Opened by glabilloy over 9 years ago - 1 comment

#31 - Question for X-Linked recessive case analysis

Issue - State: closed - Opened by hmkim over 9 years ago - 4 comments

#30 - Does this work for VCFs with more than one trio?

Issue - State: closed - Opened by leipzig over 9 years ago - 6 comments

#29 - genmod breaking VCF format when adding software tag to header

Issue - State: closed - Opened by tzhughes over 9 years ago - 2 comments

#28 - Sort order not respected by genmod

Issue - State: closed - Opened by tzhughes over 9 years ago - 3 comments

#27 - Analysing WG quad data- genmod

Issue - State: closed - Opened by tzhughes over 9 years ago - 29 comments

#26 - Version 1.5.19 crashing also with test data but with different error

Issue - State: closed - Opened by tzhughes over 9 years ago - 2 comments

#25 - Version 1.5.19 crashing

Issue - State: closed - Opened by tzhughes over 9 years ago - 2 comments

#24 - Implement genmod analyze

Issue - State: closed - Opened by moonso about 10 years ago - 1 comment

#23 - Add -strict flag

Issue - State: closed - Opened by moonso about 10 years ago - 1 comment

#22 - change to relative imports within package

Issue - State: closed - Opened by moonso about 10 years ago

#21 - AR_comp design

Issue - State: closed - Opened by tzhughes about 10 years ago - 16 comments

#20 - Denovo and noCalls

Issue - State: closed - Opened by tzhughes about 10 years ago - 9 comments

#19 - Stats from real data indicate that implementation of -phase is a loosening of conditions

Issue - State: closed - Opened by tzhughes about 10 years ago - 32 comments

GitHub / Clinical-Genomics/genmod issues and pull requests