Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / hammerlab/biokepi issues and pull requests

#50 - Add more alligners

Issue - State: open - Opened by smondet over 9 years ago
Labels: target library

#50 - Add more alligners

Issue - State: open - Opened by smondet over 9 years ago
Labels: target library

#49 - Add cloudbreak

Issue - State: open - Opened by smondet over 9 years ago - 2 comments
Labels: target library

#49 - Add cloudbreak

Issue - State: open - Opened by smondet over 9 years ago - 2 comments
Labels: target library

#48 - Add Platypus

Issue - State: open - Opened by smondet over 9 years ago
Labels: target library

#48 - Add Platypus

Issue - State: open - Opened by smondet over 9 years ago
Labels: target library

#47 - Create pipeline for neoepitope prediction

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

#47 - Create pipeline for neoepitope prediction

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

#46 - Make Picard MarkDuplicates spilling settings configurable

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

#46 - Make Picard MarkDuplicates spilling settings configurable

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

#45 - Experiment: `Common.KEDSL`

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

#45 - Experiment: `Common.KEDSL`

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

#44 - Add strelka to default toolkit

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

#44 - Add strelka to default toolkit

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

#43 - Fix sort by coordinate

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

#43 - Fix sort by coordinate

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

#42 - Bams in pipelines

Pull Request - State: closed - Opened by smondet over 9 years ago - 2 comments

#42 - Bams in pipelines

Pull Request - State: closed - Opened by smondet over 9 years ago - 2 comments

#41 - run indel realigner jointly for tumor/normal BAMs

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

#41 - run indel realigner jointly for tumor/normal BAMs

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

#40 - Create MuSE target

Issue - State: closed - Opened by hammer over 9 years ago - 3 comments
Labels: target library

#40 - Create MuSE target

Issue - State: closed - Opened by hammer over 9 years ago - 3 comments
Labels: target library

#39 - Add bedtools and bamtofastq

Pull Request - State: closed - Opened by arahuja over 9 years ago - 4 comments

#39 - Add bedtools and bamtofastq

Pull Request - State: closed - Opened by arahuja over 9 years ago - 4 comments

#37 - Create topiary target

Issue - State: closed - Opened by hammer over 9 years ago - 2 comments
Labels: target library

#37 - Create topiary target

Issue - State: closed - Opened by hammer over 9 years ago - 2 comments
Labels: target library

#36 - Adding multi-threading option to GATK tools

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

#36 - Adding multi-threading option to GATK tools

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

#35 - BQSR keeps hitting missing file

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

#35 - BQSR keeps hitting missing file

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

#34 - Setup tool versioning

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

#34 - Setup tool versioning

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

#33 - Add HLA typing

Issue - State: closed - Opened by arahuja over 9 years ago - 2 comments
Labels: target library

#33 - Add HLA typing

Issue - State: closed - Opened by arahuja over 9 years ago - 2 comments
Labels: target library

#32 - Add hg18 reference

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

#32 - Add hg18 reference

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

#31 - remove sam after creating bam

Pull Request - State: closed - Opened by arahuja over 9 years ago - 2 comments

#31 - remove sam after creating bam

Pull Request - State: closed - Opened by arahuja over 9 years ago - 2 comments

#30 - Support Guacamole

Issue - State: open - Opened by smondet over 9 years ago - 6 comments

#30 - Support Guacamole

Issue - State: open - Opened by smondet over 9 years ago - 6 comments

#29 - Sort and convert sam to bam simultaneously

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

#29 - Sort and convert sam to bam simultaneously

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

#27 - BQSR doesn't work with B38 build

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

#27 - BQSR doesn't work with B38 build

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

#26 - Move bam type to Dna_bam and add Rna_bam

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

#26 - Move bam type to Dna_bam and add Rna_bam

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

#25 - Make processors a max_procesors argument to a machine

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

#25 - Make processors a max_procesors argument to a machine

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

#24 - Make the reference-build a property of the BAM

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

#24 - Make the reference-build a property of the BAM

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

#23 - Allow mutect to specify a BED/VCF file for intervals

Issue - State: open - Opened by arahuja over 9 years ago

#23 - Allow mutect to specify a BED/VCF file for intervals

Issue - State: open - Opened by arahuja over 9 years ago

#22 - Add haplotype caller from GATK

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

#22 - Add haplotype caller from GATK

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

#21 - Add b37 reference with decoy sequences

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

#21 - Add b37 reference with decoy sequences

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

#20 - add bwa mem option

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

#20 - add bwa mem option

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

#19 - Specify reference build for alignment

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

#19 - Specify reference build for alignment

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

#18 - Split targets into multiple files

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

#18 - Split targets into multiple files

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

#17 - Add travis config

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

#17 - Add travis config

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

#16 - Fix samtools sort flag

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

#16 - Fix samtools sort flag

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

#15 - Add suport for GRCh38 and hg19

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

#15 - Add suport for GRCh38 and hg19

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

#14 - give threads argument to samtools sort

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

#14 - give threads argument to samtools sort

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

#13 - ensure working dir in strelka

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

#13 - ensure working dir in strelka

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

#12 - Ensure result directories exist

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

#12 - Ensure result directories exist

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

#11 - add sorting and indexing of bams as dependency to strelka

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

#11 - add sorting and indexing of bams as dependency to strelka

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

#10 - Add BWA-MEM to target library

Issue - State: closed - Opened by hammer over 9 years ago
Labels: target library

#10 - Add BWA-MEM to target library

Issue - State: closed - Opened by hammer over 9 years ago
Labels: target library

#9 - Factor somatic variant callers in the same GADT variant

Pull Request - State: closed - Opened by smondet over 9 years ago - 5 comments

#9 - Factor somatic variant callers in the same GADT variant

Pull Request - State: closed - Opened by smondet over 9 years ago - 5 comments

#8 - Add support for BASSOVAC

Issue - State: open - Opened by hammer over 9 years ago - 3 comments
Labels: target library

#8 - Add support for BASSOVAC

Issue - State: open - Opened by hammer over 9 years ago - 3 comments
Labels: target library

#7 - install through OPAM

Issue - State: closed - Opened by arahuja over 9 years ago - 8 comments

#6 - Add GATK haplotype caller to target library

Issue - State: closed - Opened by arahuja over 9 years ago - 1 comment
Labels: target library

#5 - Add Virmid (target-lib, pipeline, and tool)

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

#4 - Expose more parameters for variant callers

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

#3 - Add Strelka pipeline step

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

#2 - Add SNAP to target library

Issue - State: open - Opened by hammer almost 10 years ago
Labels: target library

#1 - Reviewed README.md

Pull Request - State: closed - Opened by rleonid almost 10 years ago - 1 comment