Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / populationgenomics/joint-calling issues and pull requests
#92 - Renames get_sequences_by_sample_ids to *_for_sample_ids
Pull Request -
State: closed - Opened by illusional almost 2 years ago
- 2 comments
#91 - Add NA12878 validation notebook
Pull Request -
State: closed - Opened by vladsavelyev over 2 years ago
#90 - Fix license description
Pull Request -
State: closed - Opened by lgruen over 2 years ago
#89 - [join-calling]: use transmitted singletons
Issue -
State: open - Opened by vladsavelyev over 2 years ago
Labels: enhancement
#88 - [large-cohort] Document variant filtering
Issue -
State: open - Opened by vladsavelyev over 2 years ago
Labels: documentation
#87 - [population pipeline] NAGIM: prepare amp-pd+mgrb subset for Joe Copty
Issue -
State: open - Opened by vladsavelyev over 2 years ago
Labels: question
#86 - [population pipeline] Benchmark NAGIM run
Issue -
State: open - Opened by vladsavelyev over 2 years ago
- 1 comment
Labels: documentation
#85 - Make release VCF. Nagim. Support relateds. SM 4.0.0. Add X het/hom ratio and freqs
Pull Request -
State: closed - Opened by vladsavelyev almost 3 years ago
#84 - Update sm api
Pull Request -
State: closed - Opened by vivbak almost 3 years ago
#83 - Fix no value for param
Pull Request -
State: closed - Opened by vivbak almost 3 years ago
#82 - PCA plots: use external IDs, fix double counting
Pull Request -
State: closed - Opened by vladsavelyev almost 3 years ago
#81 - Update PCA plots, fix PED file, check existence flags
Pull Request -
State: closed - Opened by vladsavelyev almost 3 years ago
#80 - Incorporate gene names into hover tools.
Pull Request -
State: closed - Opened by KatalinaBobowik almost 3 years ago
#79 - Add Somalier for relatedness checks
Pull Request -
State: closed - Opened by vladsavelyev about 3 years ago
#78 - Move more requester-pay files & fix in PCA plot
Pull Request -
State: closed - Opened by vladsavelyev about 3 years ago
#77 - Fix Unit Tests
Pull Request -
State: closed - Opened by vivbak about 3 years ago
- 1 comment
#76 - Move requester-pays ref files
Pull Request -
State: closed - Opened by vladsavelyev about 3 years ago
#75 - Add validation samples. Add alignment and haplotypecaller.
Pull Request -
State: closed - Opened by vladsavelyev about 3 years ago
#74 - Integrate ancestry
Pull Request -
State: closed - Opened by vladsavelyev about 3 years ago
- 1 comment
#73 - Sample QC refactoring (mostly `pc_relate`)
Pull Request -
State: closed - Opened by vladsavelyev about 3 years ago
#72 - Split `sample_qc.py` into `sample_qc_calculate.py` and `sample_qc_write_metadata.py`
Pull Request -
State: closed - Opened by vladsavelyev about 3 years ago
#71 - Sample QC: use non-preemptible workers
Pull Request -
State: closed - Opened by vladsavelyev about 3 years ago
#70 - Fix setting up workers disk
Pull Request -
State: closed - Opened by vladsavelyev about 3 years ago
#69 - More disk for sample_qc
Pull Request -
State: closed - Opened by vladsavelyev about 3 years ago
#68 - Add tmp dir for VQSR
Pull Request -
State: closed - Opened by vladsavelyev about 3 years ago
#67 - More space for Apply VQSR job
Pull Request -
State: closed - Opened by vladsavelyev about 3 years ago
#66 - Various SM communication fixes
Pull Request -
State: closed - Opened by vladsavelyev about 3 years ago
#65 - Run joint-calling from this repo rather than tob-wgs
Pull Request -
State: closed - Opened by vladsavelyev about 3 years ago
#64 - Read data from the SM server
Pull Request -
State: closed - Opened by vladsavelyev about 3 years ago
#63 - Fix merge
Pull Request -
State: closed - Opened by vivbak about 3 years ago
#62 - Fix reads
Pull Request -
State: closed - Opened by vivbak about 3 years ago
#61 - Fix Request
Pull Request -
State: closed - Opened by vivbak about 3 years ago
#60 - Add 300 cap
Pull Request -
State: closed - Opened by vivbak about 3 years ago
#59 - Split mt, add `snps_not_on_gnomad`, move ref files
Pull Request -
State: closed - Opened by vladsavelyev about 3 years ago
- 1 comment
#58 - remove sm_project, replace with project
Pull Request -
State: closed - Opened by vivbak about 3 years ago
#57 - Pull latest inputs using SM API
Pull Request -
State: closed - Opened by vivbak about 3 years ago
- 1 comment
#56 - Broad issue to track the joint-calling workflow improvement
Issue -
State: open - Opened by vladsavelyev about 3 years ago
#55 - Fix md5 check
Pull Request -
State: closed - Opened by vivbak about 3 years ago
#54 - Fix according to analysis runner update
Pull Request -
State: closed - Opened by vivbak about 3 years ago
#53 - Matrix table output updates
Pull Request -
State: closed - Opened by vladsavelyev about 3 years ago
- 1 comment
#52 - Add storage for hl.export_vcf
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
#51 - Integrate sample metadata API
Pull Request -
State: closed - Opened by vivbak over 3 years ago
- 3 comments
#50 - Refactor docstrings
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
#49 - ReblockGVCFs: keep low quals
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
#48 - Validate MD5
Pull Request -
State: closed - Opened by vivbak over 3 years ago
#47 - Add comment about spanning del, fix `AS_SB_TABLE` parsing, fix overwriting
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
#46 - Refactor mt_to_vcf
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
- 2 comments
#45 - Fix & refactor combining with existing matrix table
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
#44 - Write metadata to new metadata buckets
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
#43 - Adapt upload processor to new metadata buckets
Pull Request -
State: closed - Opened by lgruen over 3 years ago
#42 - Be explicit about the number of partitions. Make --scatter-count required
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
#41 - More fix bucket suffixes
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
#40 - Update bucket pointers
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
#39 - Add option to set the number of workers for dataproc
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
#38 - Start counting batches from 1
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
#37 - Disable trios, make tests pass
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
- 1 comment
#36 - VQSR: filter INFO/SB field out broken by GATK
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
- 1 comment
#35 - Extract `create_rf_annotations.py` from `random_forest.py`
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
#34 - Support run to test. Fix filtering cutoffs. Fix exporting VQSR to Hail.
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
#33 - Generalise processor
Pull Request -
State: closed - Opened by vivbak over 3 years ago
#32 - Update docker image
Pull Request -
State: closed - Opened by vivbak over 3 years ago
#31 - Add service backend
Pull Request -
State: closed - Opened by vivbak over 3 years ago
#30 - Initialise Hail
Pull Request -
State: closed - Opened by vivbak over 3 years ago
#29 - fix file path
Pull Request -
State: closed - Opened by vivbak over 3 years ago
#28 - Add init file
Pull Request -
State: closed - Opened by vivbak over 3 years ago
#27 - Add shebang
Pull Request -
State: closed - Opened by vivbak over 3 years ago
#26 - Run upload processor on TOB-WGS uploads
Pull Request -
State: closed - Opened by vivbak over 3 years ago
- 2 comments
#25 - Batch workflow. Add RF and VQSR
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
- 3 comments
#24 - Add RF and VQSR
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
#23 - Joint-calling batch workflow
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
#22 - Add authenticate and filter
Pull Request -
State: open - Opened by vivbak over 3 years ago
#21 - CI refactor
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
#20 - Move Files
Pull Request -
State: closed - Opened by vivbak over 3 years ago
- 1 comment
#19 - Add filter-callrate
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
#18 - Rename to joint-calling
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
#17 - Authenticate and connect upload processor to airtable
Pull Request -
State: closed - Opened by vivbak over 3 years ago
#16 - Fixing minor typos
Pull Request -
State: closed - Opened by pdiakumis over 3 years ago
#15 - Update usage with dataproc in README. Fix typos. Reuse in combiner.
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
#14 - Sample QC / joint caller workflow tests
Issue -
State: open - Opened by vladsavelyev over 3 years ago
#13 - Scale VCF combiner workflow
Issue -
State: open - Opened by vladsavelyev over 3 years ago
#12 - Update git clone
Pull Request -
State: closed - Opened by vivbak over 3 years ago
#11 - Upload Processor
Issue -
State: open - Opened by vivbak over 3 years ago
- 1 comment
#10 - My new docs
Pull Request -
State: closed - Opened by illusional over 3 years ago
#9 - Convert VQSR pipeline to Batch
Issue -
State: closed - Opened by illusional over 3 years ago
- 2 comments
#8 - Add framework for VQSR
Pull Request -
State: closed - Opened by illusional over 3 years ago
- 4 comments
#7 - install conda dependencies first
Pull Request -
State: closed - Opened by pdiakumis over 3 years ago
#6 - Adding VQSR to the QC pipeline
Issue -
State: closed - Opened by illusional over 3 years ago
- 1 comment
#5 - Combiner: support extending
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
- 3 comments
#4 - Add linting & refactor
Pull Request -
State: closed - Opened by vladsavelyev over 3 years ago
#3 - Add sample QC, CI, tests
Pull Request -
State: closed - Opened by vladsavelyev almost 4 years ago
- 4 comments
#2 - Implement basic sample and variant QC
Issue -
State: closed - Opened by lgruen almost 4 years ago
- 1 comment
#1 - Verify Hail's vcf_combiner functionality
Issue -
State: closed - Opened by lgruen almost 4 years ago
- 4 comments