https://github.com/rbpisupati/nf-haplocaller

Nextflow pipeline for GATK best practices (HaplotypeCaller)
https://github.com/rbpisupati/nf-haplocaller

awesome-nextflow gatk haplotypecaller nextflow snp-calling

Last synced: about 2 months ago
JSON representation

Nextflow pipeline for GATK best practices (HaplotypeCaller)

• Host: GitHub
• URL: https://github.com/rbpisupati/nf-haplocaller
• Owner: rbpisupati
• License: mit
• Created: 2018-12-14T09:31:23.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2019-07-16T08:01:15.000Z (over 5 years ago)
• Last Synced: 2023-10-20T22:47:19.053Z (about 1 year ago)
• Topics: awesome-nextflow, gatk, haplotypecaller, nextflow, snp-calling
• Language: Nextflow
• Homepage:
• Size: 17.6 KB
• Stars: 1
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
# Nextflow pipeline for GATK best practices, SNP calling

## Installation

This pipeline itself needs no installation - NextFlow will automatically fetch it from GitHub rbpisupati/nf-haplocaller

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.

```bash

git clone https://github.com/rbpisupati/nf-haplocaller.git

```

## Running the pipeline

```bash

nextflow run nf-haplocaller/main.nf --reads "*bam" --fasta "TAIR10_wholeGenome.fasta" --outdir output_folder

```

Add `--notrim false` to include trimming of the reads. Also you can change the trimming parameters

## Credits

- Rahul Pisupati (rahul.pisupati[at]gmi.oeaw.ac.at)

## Citation

Cite the paper below if you use this pipeline.

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)