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- Overview
- installation
- small cohorts (n < ~ 40)
- population calling
- Troubleshooting
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smoove simplifies and speeds calling and genotyping SVs for short reads. It also improves specificity by removing many spurious alignment signals that are indicative of low-level noise and often contribute to spurious calls.
There is a blog-post describing smoove in more detail here
It both supports small cohorts in a single command, and population-level calling with 4 total steps, 2 of which are parallel by sample.
There is a table on the precision and recall of smoove and duphold (which is used by smoove)here
It requires:
•lumpy and lumpy_filter
you can get smoove and all dependencies via (a large) docker image:
Or, you can download a smoove binary from here: https://github.com/brentp/smoove/releases When run without any arguments, smoove will show you which of it's dependencies it can find so you can adjust your $PATH and install accordingly.
for small cohorts it's possible to get a jointly-called, genotyped VCF in a single command.
output will go to ./my-cohort-smoove.genotyped.vcf.gz
the --exclude $bed is highly recommended as it can be used to ignore reads that overlap problematic regions.
A good set of regions for GRCh37 is here.
For population-level calling (large cohorts) the steps are:
1.For each sample, call genotypes:
For large cohorts, it's better to parallelize across samples rather than using a large $threads per sample. smoove can only parallelize up to 2 or 3 threads on a single-sample and it's most efficient to use 1 thread.
output will go to `results-smoove/$sample-smoove.genotyped.vcf.gz``
1.Get the union of sites across all samples (this can parallelize this across as many CPUs or machines as needed):
1.genotype each sample at those sites (this can parallelize this across as many CPUs or machines as needed) and run duphold to add depth annotations.
•A panic with a message like Segmentation fault (core dumped) | bcftools view -O z -c 1 -o is likely to mean you have an old version of bcftools. see #10
•smoove will write to the system TMPDIR. For large cohorts, make sure to set this to something with a lot of space. e.g. export TMPDIR=/path/to/big
smoove is a Go program that simplifies and speeds calling and genotyping SVs for short reads. It uses lumpy, lumpy_filter, svtyper, and other tools to improve specificity and efficiency.
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Apr 12, 2018 · smoove is a tool that helps you create and publish landing pages for your marketing campaigns. You can customize your pages with drag-and-drop interface, smart blocks, web forms, personalization fields and more.
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