Using Curio for Variant Analysis
Curio's approach to analyzing aligned NGS sequence data to find potential variants can be logically thought of as two phases.
The first phase involves running an analysis to detect where potential
variants exist in one or more samples, and the second phase involves using the output of those analyses to
filter down the variants you're interested in within a single sample
or by comparing the analysis of two or more samples to each other.
E.g. if you had several samples, some that represent the control (perhaps the germline) and some that represent the
experimental samples of one or more particular tissues, you could ask Curio to detect somatic variants in the experimental tissue
by doing the following:
- Detect variants in the control sample(s)
- Detect variants in the experimental tissue sample(s)
- Find the somatic variants by filtering the variants from analysis #1 out of those found in analysis #2, taking into
account the read coverage in each
Curio supports an intuitive way to control both how the variants are detected in the first phase across one or more
samples, and similarly allows you to visualize in real time how changes to different filter settings affect the
resulting variants in the second phase. And, in addition to somatic filtering, Curio provides other ways to
compare multiple samples to one another, such as looking for variants that are in common across multiple samples.
Also, when looking at the filtered variants you can bring in other annotations that are relevant to the
resulting variants (including filtering by genomic region type or predicted amino acid changes) as well as export
the full list of variants in different forms (VCF, CSV).
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