Ecosyste.ms: Issues

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GitHub / clinical-genomics/balsamic issues and pull requests

#99 - MultiQC

Issue - State: closed - Opened by hassanfa over 6 years ago - 1 comment
Labels: Feature

#99 - MultiQC

Issue - State: closed - Opened by hassanfa over 6 years ago - 1 comment
Labels: Feature

#98 - Config changes for production

Pull Request - State: closed - Opened by hassanfa over 6 years ago

#98 - Config changes for production

Pull Request - State: closed - Opened by hassanfa over 6 years ago

#97 - Rule changes on how fastq files are handled

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Feature

#97 - Rule changes on how fastq files are handled

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Feature

#96 - BALSAMIC run command changes

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Feature

#96 - BALSAMIC run command changes

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Feature

#95 - Config file changes to production

Issue - State: closed - Opened by hassanfa over 6 years ago - 2 comments
Labels: Feature

#95 - Config file changes to production

Issue - State: closed - Opened by hassanfa over 6 years ago - 2 comments
Labels: Feature

#94 - Directory structure

Issue - State: closed - Opened by hassanfa over 6 years ago - 3 comments
Labels: Feature

#94 - Directory structure

Issue - State: closed - Opened by hassanfa over 6 years ago - 3 comments
Labels: Feature

#93 - Ti/Tv transition to transversion calculations

Issue - State: closed - Opened by hassanfa over 6 years ago - 2 comments

#93 - Ti/Tv transition to transversion calculations

Issue - State: closed - Opened by hassanfa over 6 years ago - 2 comments

#92 - Config file overwrites without prompt

Issue - State: closed - Opened by hassanfa over 6 years ago - 1 comment
Labels: Bug

#92 - Config file overwrites without prompt

Issue - State: closed - Opened by hassanfa over 6 years ago - 1 comment
Labels: Bug

#91 - Link fastq files within analysis directory

Issue - State: closed - Opened by hassanfa over 6 years ago - 1 comment
Labels: Feature

#91 - Link fastq files within analysis directory

Issue - State: closed - Opened by hassanfa over 6 years ago - 1 comment
Labels: Feature

#90 - Panel of normals for Mutect2

Issue - State: closed - Opened by hassanfa over 6 years ago - 1 comment
Labels: Feature

#90 - Panel of normals for Mutect2

Issue - State: closed - Opened by hassanfa over 6 years ago - 1 comment
Labels: Feature

#89 - Second aligner to reduce artifacts risen from mapping algorithms

Issue - State: closed - Opened by hassanfa over 6 years ago - 2 comments

#89 - Second aligner to reduce artifacts risen from mapping algorithms

Issue - State: closed - Opened by hassanfa over 6 years ago - 2 comments

#88 - Picard QC runs after and before markduplicate

Issue - State: closed - Opened by hassanfa over 6 years ago - 1 comment
Labels: Feature

#88 - Picard QC runs after and before markduplicate

Issue - State: closed - Opened by hassanfa over 6 years ago - 1 comment
Labels: Feature

#87 - Bedsplit bug fix

Pull Request - State: closed - Opened by hassanfa over 6 years ago

#87 - Bedsplit bug fix

Pull Request - State: closed - Opened by hassanfa over 6 years ago

#86 - parsed picard markdup is badly formatted

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Bug

#86 - parsed picard markdup is badly formatted

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Bug

#85 - splitbed fails on non-standard chromosome id

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Bug

#85 - splitbed fails on non-standard chromosome id

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Bug

#84 - Downsampling fq files for QC and Alignment workflow

Issue - State: closed - Opened by hassanfa over 6 years ago - 2 comments
Labels: Feature, Gain Large, Effort Medium, Urgency Small

#84 - Downsampling fq files for QC and Alignment workflow

Issue - State: closed - Opened by hassanfa over 6 years ago - 2 comments
Labels: Feature, Gain Large, Effort Medium, Urgency Small

#83 - Report fix

Pull Request - State: closed - Opened by hassanfa over 6 years ago

#83 - Report fix

Pull Request - State: closed - Opened by hassanfa over 6 years ago

#82 - Sambamba depth param stepify! 😯

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Feature

#82 - Sambamba depth param stepify! 😯

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Feature

#81 - Some rmdup and mrkdup flags are set differently

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Bug

#81 - Some rmdup and mrkdup flags are set differently

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Bug

#80 - Add logger

Issue - State: closed - Opened by hassanfa over 6 years ago - 1 comment
Labels: Feature

#80 - Add logger

Issue - State: closed - Opened by hassanfa over 6 years ago - 1 comment
Labels: Feature

#79 - QOS in balsamic run cli

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Feature

#79 - QOS in balsamic run cli

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Feature

#78 - Sample config generation fastq checks

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Feature

#78 - Sample config generation fastq checks

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Feature

#77 - Installation patch

Pull Request - State: closed - Opened by hassanfa over 6 years ago

#77 - Installation patch

Pull Request - State: closed - Opened by hassanfa over 6 years ago

#76 - Germline calling for filtering out reads in paired mode

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

#76 - Germline calling for filtering out reads in paired mode

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

#75 - Add plot functionality to coverage report script

Issue - State: closed - Opened by hassanfa over 6 years ago - 1 comment
Labels: Feature

#75 - Add plot functionality to coverage report script

Issue - State: closed - Opened by hassanfa over 6 years ago - 1 comment
Labels: Feature

#74 - BALSAMIC extension for statusDB

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

#74 - BALSAMIC extension for statusDB

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

#73 - UMI support for BALSAMIC

Issue - State: closed - Opened by hassanfa over 6 years ago - 2 comments
Labels: Feature

#73 - UMI support for BALSAMIC

Issue - State: closed - Opened by hassanfa over 6 years ago - 2 comments
Labels: Feature

#72 - Replace normalizing and left align variants using vt

Issue - State: closed - Opened by hassanfa over 6 years ago - 1 comment
Labels: Feature

#72 - Replace normalizing and left align variants using vt

Issue - State: closed - Opened by hassanfa over 6 years ago - 1 comment
Labels: Feature

#71 - Variant reporter patch

Pull Request - State: closed - Opened by hassanfa over 6 years ago

#71 - Variant reporter patch

Pull Request - State: closed - Opened by hassanfa over 6 years ago

#69 - shit -> shift

Issue - State: closed - Opened by hassanfa over 6 years ago

#69 - shit -> shift

Issue - State: closed - Opened by hassanfa over 6 years ago

#68 - Coverage report sometimes returns 0 coverage for all genes

Issue - State: closed - Opened by hassanfa over 6 years ago - 5 comments
Labels: Bug

#68 - Coverage report sometimes returns 0 coverage for all genes

Issue - State: closed - Opened by hassanfa over 6 years ago - 5 comments
Labels: Bug

#67 - Report mapping quality in mutect2

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Feature

#67 - Report mapping quality in mutect2

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Feature

#66 - VCF union and fixes

Pull Request - State: closed - Opened by hassanfa over 6 years ago

#66 - VCF union and fixes

Pull Request - State: closed - Opened by hassanfa over 6 years ago

#65 - create_config doesn't create config file properly if path does not exist.

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Bug

#65 - create_config doesn't create config file properly if path does not exist.

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Bug

#64 - Reporting actual DP and AD in Mutect2

Issue - State: closed - Opened by hassanfa over 6 years ago - 3 comments
Labels: Bug, Feature

#64 - Reporting actual DP and AD in Mutect2

Issue - State: closed - Opened by hassanfa over 6 years ago - 3 comments
Labels: Bug, Feature

#63 - PASS filter remove from Strelka

Issue - State: closed - Opened by hassanfa over 6 years ago - 1 comment
Labels: Bug

#63 - PASS filter remove from Strelka

Issue - State: closed - Opened by hassanfa over 6 years ago - 1 comment
Labels: Bug

#62 - Result report filter config

Issue - State: closed - Opened by hassanfa over 6 years ago - 2 comments
Labels: Feature

#62 - Result report filter config

Issue - State: closed - Opened by hassanfa over 6 years ago - 2 comments
Labels: Feature

#61 - Merge caller VCF - paired mode

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Feature

#61 - Merge caller VCF - paired mode

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Feature

#60 - Coverage patch

Pull Request - State: closed - Opened by hassanfa over 6 years ago

#60 - Coverage patch

Pull Request - State: closed - Opened by hassanfa over 6 years ago

#59 - Single mode config bug fix

Pull Request - State: closed - Opened by hassanfa over 6 years ago

#59 - Single mode config bug fix

Pull Request - State: closed - Opened by hassanfa over 6 years ago

#58 - json_out should be swapped with output_config to properly create the path.

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Bug

#58 - json_out should be swapped with output_config to properly create the path.

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Bug

#57 - scratch and TMPDIR fix for _very_ large bam file

Issue - State: closed - Opened by hassanfa over 6 years ago - 2 comments
Labels: Feature

#56 - Manta single sample mode

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Bug

#56 - Manta single sample mode

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Bug

#55 - Structural variant visualization

Issue - State: closed - Opened by hassanfa over 6 years ago

#55 - Structural variant visualization

Issue - State: closed - Opened by hassanfa over 6 years ago

#54 - Remove strelka from json config file for single sample

Issue - State: closed - Opened by keyvanelhami over 6 years ago
Labels: Bug

#54 - Remove strelka from json config file for single sample

Issue - State: closed - Opened by keyvanelhami over 6 years ago
Labels: Bug

#53 - Variant calling AF threshold for Vardict as a parameter in config

Issue - State: closed - Opened by hassanfa over 6 years ago - 1 comment
Labels: Feature

#53 - Variant calling AF threshold for Vardict as a parameter in config

Issue - State: closed - Opened by hassanfa over 6 years ago - 1 comment
Labels: Feature

#52 - Remove/mark duplicate as a flag in config

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Feature

#52 - Remove/mark duplicate as a flag in config

Issue - State: closed - Opened by hassanfa over 6 years ago
Labels: Feature

#51 - Tumor mutational burden

Issue - State: closed - Opened by hassanfa over 6 years ago - 4 comments
Labels: Feature

#51 - Tumor mutational burden

Issue - State: closed - Opened by hassanfa over 6 years ago - 4 comments
Labels: Feature

#50 - Add flag for mark duplicate in the config file

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