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

#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

#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

#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

#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

#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

#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