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Nextflow pipeline for GATK best practices (HaplotypeCaller)
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rbpisupati/nf-haplocaller
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This pipeline itself needs no installation - NextFlow will automatically fetch it from GitHub rbpisupati/nf-haplocallerThe 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
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
- Rahul Pisupati (rahul.pisupati[at]gmi.oeaw.ac.at)
Cite the paper below if you use this pipeline.Pisupati, R.et al.. Verification ofArabidopsis stock collections using SNPmatch, a tool for genotyping high-plexed samples.Nature Scientific Data4, 170184 (2017).doi:10.1038/sdata.2017.184
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Nextflow pipeline for GATK best practices (HaplotypeCaller)
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