For this exercise we will use the epi2me-labs/wf-human-variation pipeline. Find information on the pipeline at https://labs.epi2me.io/workflows/wf-human-variation/
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Approximate run time: Variable depending on whether it is targeted sequencing or whole genome sequencing, as well as coverage and the individual analyses requested. For instance, a 90X human sample run (options: --snp --sv --mod --str --cnv --phased --sex male) takes less than 8h with recommended resources.
NOTE: in contrast to the nf-core/sarek pipeline that we used in session 2, the epi2me-labs/wf-human-variation pipeline runs in ‘local’ mode (needs large amount of CPUs and RAM memory), while the nf-core/sarek pipeline will use a ‘pbspro’ mode, where the pipeline will submit individual jobs to the HPC cluster and define the CPUs and memory for each task individually.
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Monitor the progress of the job:
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qjobs |
Once the pipeline has complete you will see the following set of output files in the ‘results’ folder:
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.
├── DEMO.flagstat.tsv
├── DEMO.mosdepth.global.dist.txt
├── DEMO.mosdepth.summary.txt
├── DEMO.readstats.tsv.gz
├── DEMO.regions.bed.gz
├── DEMO.stats.json
├── DEMO.thresholds.bed.gz
├── DEMO.wf-human-alignment-report.html
├── DEMO.wf-human-snp-report.html
├── DEMO.wf-human-sv-report.html
├── DEMO.wf_snp_clinvar.vcf
├── DEMO.wf_snp.vcf.gz
├── DEMO.wf_snp.vcf.gz.tbi
├── DEMO.wf_sv.vcf.gz
├── DEMO.wf_sv.vcf.gz.tbi
├── execution
│ ├── report.html
│ ├── timeline.html
│ └── trace.txt
├── jbrowse.json
└── OPTIONAL_FILE |