https://github.com/kids-first/kf-genotype-refinement-workflow
https://github.com/kids-first/kf-genotype-refinement-workflow
bioinformatics cwl
Last synced: 4 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/kids-first/kf-genotype-refinement-workflow
- Owner: kids-first
- Created: 2018-07-06T17:23:14.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2019-11-19T21:01:34.000Z (over 6 years ago)
- Last Synced: 2023-02-28T03:23:09.668Z (over 3 years ago)
- Topics: bioinformatics, cwl
- Language: Common Workflow Language
- Size: 295 KB
- Stars: 1
- Watchers: 8
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# kfdrc genotype refinement workflow
## Implementation of Broad Institute Genotype Refinement Workflow
Genotype Refinement workflow for germline short variants
+ Note, step 4 is skipped
+ variant effect predictor run at the end to annotate vcf and get variant summary stats
## basic info
- tool images: https://hub.docker.com/r/kfdrc/
- dockerfiles: https://github.com/d3b-center/bixtools
- tested with
- rabix-v1.0.5: https://github.com/rabix/bunny/releases/tag/v1.0.5
## inputs:
+ Uses output gvcf from https://github.com/kids-first/kf-jointgenotyping-workflow
```yaml
ped:
class: File
path: FM_XXXXXX.ped
reference:
class: File
path: Homo_sapiens_assembly38.fasta
cache: File
class: File
path: homo_sapiens_vep_93_GRCh38_convert_cache.tar.gz # tar gzipped vep93 cache file
snp_sites:
class: File
path: 1000G_phase3_v4_20130502.sites.hg38.vcf
vqsr_vcf:
class: File
path: vqsr_vcf.vcf.gz # A recalibrated variants gvcf from VQSR
output_basename: vqsr_vcf
```
