https://github.com/rbpisupati/nf-snpmatch
Nextflow pipeline for SNPmatch (https://github.com/Gregor-Mendel-Institute/SNPmatch.git)
https://github.com/rbpisupati/nf-snpmatch
1001genomes arabidopsis arageno genotyping-by-sequencing nextflow snpmatch
Last synced: 29 days ago
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Nextflow pipeline for SNPmatch (https://github.com/Gregor-Mendel-Institute/SNPmatch.git)
- Host: GitHub
- URL: https://github.com/rbpisupati/nf-snpmatch
- Owner: rbpisupati
- Created: 2018-08-30T13:58:34.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2022-04-01T08:21:42.000Z (over 3 years ago)
- Last Synced: 2024-12-26T13:26:30.425Z (10 months ago)
- Topics: 1001genomes, arabidopsis, arageno, genotyping-by-sequencing, nextflow, snpmatch
- Language: Nextflow
- Size: 62.5 KB
- Stars: 0
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Nextflow pipeline for running SNPmatch
## Installation
This pipeline itself needs no installation - NextFlow will automatically fetch it from GitHub rbpisupati/nf-snpmatch
```bash
git clone https://github.com/rbpisupati/nf-snpmatch.git
```
You need to have SNPmatch installed in your system. Please visit (https://github.com/Gregor-Mendel-Institute/SNPmatch.git) for detailed instructions on installing SNPmatch.
## Running the pipeline
### Genotyping inbred lines
```bash
nextflow run main.nf --func "inbred" --input "*.vcf" --outdir "snpmatch" --db "hdf5" --db_acc "hdf5_acc"
## or run cross genotyper
nextflow run main.nf --func "cross" --input "*.vcf" --outdir "snpmatch" --db "hdf5" --db_acc "hdf5_acc"
```
### Genotyping crosses in windows given parents
```bash
nextflow run genocross.nf --input "*.vcf" --parents "6191x6046" --window 300000 --outdir "snpmatch" --db "hdf5_path" --db_acc "hdf5_acc_path"
```
Input, parents, outdir are required arguments.
## Configuration
The pipeline is written mainly to run SNPmatch on GMI HPC mendel which is PBS system. Please change config file accordingly to run it on your system.
## Credits
- Rahul Pisupati (rahul.pisupati[at]gmi.oeaw.ac.at)
## Citation
Cite the paper below if you use SNPmatch tool.
Pisupati, R. *et al.*. Verification of *Arabidopsis* stock collections using SNPmatch, a tool for genotyping high-plexed samples. *Nature Scientific Data* **4**, 170184 (2017).
[doi:10.1038/sdata.2017.184](https://www.nature.com/articles/sdata2017184)