clinical-genomics/mip issues and pull requests

#99 - bioconda version of VEP

Issue - State: closed - Opened by robinandeer almost 9 years ago - 6 comments

#98 - Add SequencingType to qc_sampleInfo

Issue - State: closed - Opened by henrikstranneheim almost 9 years ago - 1 comment
Labels: Enhancement

#97 - Make PL in @RG information dynamic

Issue - State: closed - Opened by henrikstranneheim almost 9 years ago
Labels: Enhancement

#96 - Add support for LB in @RG information

Issue - State: closed - Opened by henrikstranneheim almost 9 years ago - 1 comment
Labels: Enhancement

#95 - Support for hg38 from fastq to ranked variants

Issue - State: open - Opened by henrikstranneheim almost 9 years ago - 6 comments

#94 - Update references

Issue - State: closed - Opened by henrikstranneheim almost 9 years ago - 1 comment

#93 - MIP install and perlbrew

Issue - State: closed - Opened by robinandeer about 9 years ago - 1 comment

#92 - Update VEP

Issue - State: closed - Opened by henrikstranneheim about 9 years ago - 1 comment

#91 - Add MTAF and MT to rank model

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

#90 - Update samtools

Issue - State: closed - Opened by henrikstranneheim about 9 years ago - 1 comment

#89 - Update Chanjo

Issue - State: closed - Opened by henrikstranneheim about 9 years ago - 1 comment

#88 - Update Plink

Issue - State: closed - Opened by henrikstranneheim about 9 years ago - 1 comment

#87 - Update vcfTools

Issue - State: closed - Opened by henrikstranneheim about 9 years ago - 1 comment

#86 - Samplecheck test fails for single cases (plink)

Issue - State: closed - Opened by emmser about 9 years ago - 1 comment

#85 - more conda installables

Issue - State: closed - Opened by robinandeer about 9 years ago - 1 comment

#84 - MIP version number in QC sample info?

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

#83 - Added reduce penetrance alternative to genmod

Issue - State: closed - Opened by henrikstranneheim about 9 years ago - 1 comment
Labels: Enhancement

#82 - SPIDEX

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

#81 - % Mapped reads in qc-metrics

Issue - State: closed - Opened by emmser about 9 years ago - 2 comments
Labels: Enhancement

#80 - Weird variant call/ranking

Issue - State: closed - Opened by robinandeer about 9 years ago - 6 comments

#79 - Issue in VEP for chromosome Y

Issue - State: closed - Opened by robinandeer about 9 years ago - 3 comments

#78 - Central log file

Issue - State: closed - Opened by robinandeer about 9 years ago - 1 comment

#77 - Overlapping read pairs

Issue - State: closed - Opened by robinandeer about 9 years ago - 1 comment

#76 - Gender Check based on all sources of gender information

Issue - State: closed - Opened by emmser about 9 years ago - 1 comment
Labels: Enhancement

#75 - Chanjo 3 support

Issue - State: closed - Opened by robinandeer over 9 years ago - 7 comments

#74 - Update SNPEff

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

#73 - Update VT

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 2 comments
Labels: Enhancement

#72 - Update picardtools

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

#71 - Update sambamba

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 2 comments
Labels: Enhancement

#70 - Update Fastqc

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 2 comments
Labels: Enhancement

#69 - Add absolute paths to clinical databases in qc_sampleInfo

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

#68 - Add rank_model file absolute path to qc_sampleInfo

Issue - State: closed - Opened by henrikstranneheim over 9 years ago

#67 - Add list of reduced penetrance genes when using genmod models

Issue - State: closed - Opened by henrikstranneheim over 9 years ago
Labels: Enhancement

#66 - Add mipLog dir to qc_sampleInfo

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 1 comment
Labels: Enhancement

#65 - Add CalculateGenoTypePosterior for trios

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 1 comment
Labels: Enhancement

#64 - Added pcrIndelModel None as default when using 'at genomes'

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 1 comment
Labels: Enhancement

#63 - Enable exome & genomes joint analysis

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 1 comment
Labels: Enhancement

#62 - Update VariantRecalibration annotations

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 1 comment
Labels: Enhancement

#61 - Update HaploTypeCaller annotations

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 1 comment
Labels: Enhancement

#60 - Make virtualenv optional?

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

#59 - Update perl 5.22

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 1 comment
Labels: Enhancement

#58 - Update VEP v.82

Issue - State: closed - Opened by henrikstranneheim over 9 years ago
Labels: Enhancement

#57 - Develop

Pull Request - State: closed - Opened by henrikstranneheim over 9 years ago

#56 - Merge branch 'release/2.4.0' into develop

Pull Request - State: closed - Opened by henrikstranneheim over 9 years ago

#55 - Update clinvar

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 1 comment
Labels: Enhancement

#54 - Update 1000G

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 1 comment
Labels: Enhancement

#53 - GATKVariantRecalibration vcf to bcf

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 1 comment
Labels: Enhancement

#52 - BEA_MEM BAM to CRAM

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 1 comment
Labels: Enhancement

#51 - Remake RemoveRedundantFiles

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 1 comment
Labels: Bug, Enhancement

#50 - Remove VariantAnnotationBlock info file from AnalysisRunStatus when -rio 0

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 1 comment
Labels: Bug

#49 - Adding a sample to pedigree does not update qc_sampleInfo for pedigreeElements for reanalysis runs

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 1 comment
Labels: Bug

#48 - Update genmod

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

#47 - Replace PicardToolsMarkDuplicates for whole genomes

Issue - State: closed - Opened by emmser over 9 years ago - 1 comment
Labels: Enhancement

#46 - ChanjoAnnotate flag in config-template seems to be defect

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

#45 - Use of display_name where relevant with MIP

Issue - State: closed - Opened by henrikstranneheim over 9 years ago

#44 - Add contig tag to clinical master list, repopulate selected contigs based on tags

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 1 comment
Labels: Bug, Enhancement

#43 - Use vt to split and normalize vt - replacing vcfparser

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

#42 - Update picardtools

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 1 comment
Labels: Enhancement

#41 - Update SNPEff

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 1 comment
Labels: Enhancement

#40 - Update VEP

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 1 comment
Labels: Enhancement

#39 - Update dbNSFP

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 1 comment
Labels: Enhancement

#38 - Update C-score database

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 1 comment
Labels: Enhancement

#37 - Update GATK version

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 3 comments
Labels: Enhancement

#36 - Add spidex database annotation

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 5 comments
Labels: Enhancement

#35 - Independent log files for all processes

Issue - State: closed - Opened by ingkebil over 9 years ago - 1 comment
Labels: Enhancement

#34 - Add population frequencies and adjust rank model to accomodate for Exac, 1000G

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 2 comments
Labels: Enhancement

#33 - Add Genetic_disease_model from clinical_list

Issue - State: closed - Opened by henrikstranneheim over 9 years ago
Labels: Enhancement

#32 - Update Genmod >2.0.6

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 1 comment
Labels: Enhancement

#31 - Add CLNACC for deep linking in Scout

Issue - State: closed - Opened by henrikstranneheim over 9 years ago - 1 comment
Labels: Enhancement

#30 - Update 1000G

Issue - State: closed - Opened by henrikstranneheim over 9 years ago
Labels: Enhancement

#29 - Update clinvar

Issue - State: closed - Opened by henrikstranneheim over 9 years ago
Labels: Enhancement

#28 - QC collect error

Issue - State: closed - Opened by robinandeer almost 10 years ago - 3 comments
Labels: Bug

#27 - AnalysisDate not set in QC sample info

Issue - State: closed - Opened by robinandeer almost 10 years ago - 2 comments

#26 - YAML key unexpectadly integer

Issue - State: closed - Opened by robinandeer almost 10 years ago - 1 comment

#25 - Absolute path in generated MIP call

Issue - State: closed - Opened by robinandeer almost 10 years ago - 1 comment

#24 - Merge pull request #23 from henrikstranneheim/master

Pull Request - State: closed - Opened by henrikstranneheim almost 10 years ago

#23 - Updating

Pull Request - State: closed - Opened by henrikstranneheim almost 10 years ago

#22 - Bugfix for GATKVarEvalExome

Pull Request - State: closed - Opened by henrikstranneheim almost 10 years ago

#21 - Develop

Pull Request - State: closed - Opened by henrikstranneheim almost 10 years ago

#20 - Merge branch 'release/2.1' into develop

Pull Request - State: closed - Opened by henrikstranneheim almost 10 years ago

#19 - Exit code, error printing and bug fix

Pull Request - State: closed - Opened by ingkebil almost 10 years ago

#18 - Incompatible command option

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

#17 - Non-standard perl installation

Issue - State: closed - Opened by robinandeer about 10 years ago - 3 comments

#16 - Migration guide/change log

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

#15 - Lock MIP to specific software versions

Issue - State: closed - Opened by robinandeer over 10 years ago - 1 comment

#14 - Open sourcing dbCMMS?

Issue - State: closed - Opened by robinandeer over 10 years ago - 1 comment

#13 - Suggestions

Issue - State: closed - Opened by robinandeer over 10 years ago - 1 comment

#12 - Family analysis error

Issue - State: closed - Opened by robinandeer over 10 years ago - 1 comment

#11 - exomeTargetBedInFileLists

Issue - State: closed - Opened by emmser almost 11 years ago - 1 comment

#10 - Updating

Pull Request - State: closed - Opened by henrikstranneheim about 11 years ago

#9 - update develop

Pull Request - State: closed - Opened by henrikstranneheim about 11 years ago

#8 - Develop

Pull Request - State: closed - Opened by henrikstranneheim over 11 years ago

#7 - Develop

Pull Request - State: closed - Opened by henrikstranneheim over 11 years ago

#6 - Added subroutine template

Pull Request - State: closed - Opened by robinandeer over 11 years ago

#5 - Added chanjo

Pull Request - State: closed - Opened by robinandeer over 11 years ago - 2 comments

#4 - nocmdinput

Issue - State: closed - Opened by robinandeer over 11 years ago - 1 comment

#3 - Integrate Cosmid database manager

Issue - State: closed - Opened by robinandeer over 11 years ago

#2 - Add Chanjo coverage analyzer

Issue - State: closed - Opened by robinandeer over 11 years ago

#1 - Pull request to update the README

Pull Request - State: closed - Opened by robinandeer over 11 years ago

GitHub / clinical-genomics/mip issues and pull requests