Aim:
Identify sequence variants using the outputs from the NextFlow: ONTprocessing pipeline. Generated minimap2 alignments are processed using https://github.com/kishwarshafin/pepper to identify highly reliable sequence variants (i.e., SNPs).
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Run the above script from within the ‘ontprocessing’ ‘ONTprocessing’ folder for the sample of interest, just outside the ‘results’ and ‘work’ folders. Once all the variables have been adjusted, run the following command:
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Check that the index file has been properly generated.
Running the ‘deepvariant’ analysis
Create a folder for the deepvariant analysis and copy the ‘index_deepvariant.csv’ file to it.
Prepare the following PBS Pro script to run the ‘deepvariant’ analysis using the minimap2 BAM files produced by the ‘ONTprocessing’ pipeline.
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#!/bin/bash -l
#PBS -N deepvariant
#PBS -l select=1:ncpus=2:mem=4gb
#PBS -l walltime=24:00:00
cd $PBS_O_WORKDIR
module load java
NXF_OPTS='-Xms1g -Xmx4g'
#run the deepvariant pipeline
nextflow run eresearchqut/deepvariant --samplesheet index_deepvariant.csv -resume
#allow access to others in the group
chmod -R g+rwX results
chmod -R g+rwX work |
Create a folder where you analyses will be run, and place a copy of both launch.pbs and index.csv in the same folder. The submit the job to the HPC cluster:
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qsub launch.pbs |
Monitor progress of the job:
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qjobs |