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.

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

Running the pipeline

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