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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Let’s inspect the HTML reports for wf-human-alignment-report.html, wf-human-snp-report.htmland wf-human-sv-report.html.
NOTE: To proceed, you need to be on QUT’s WiFi network or signed via VPN.
To browse the working folder in the HPC type in the file finder:
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| Code Block |
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├── SRR17138639.wf-human-alignment-report.html ├── SRR17138639.wf-human-snp-report.html ├── SRR17138639.wf-human-sv-report.html |
Note: transitions vs transversions (Mutations)
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Notes:
Transitions (Ti or Ts) vs transversions (Tv) mutations - typically a Whole Genome Sequencing (WGS) study finds a Ti/Tv ratio of 2.1, while exome studies detect Ti/Tv = 2.8
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ClinVar = The pipeline reports mutations overlapping known Clinical variants of interest (see:
wf-human-snp-report.html)