Bio::Sampling::Valection - Sampler for verification
Bio::Sampling::Valection contains a variety of algorithms for choosing verification candidates from competing tools or parameterizations, to fairly assess their performance against each other.
Originally created to selected from single nucleotide variant (SNV) calls generated by SNV mutation calling algorithms, this software can easily be extended to other mutation types (e.g. structural variants, gene fusions, etc.) provided data is formatted correctly.
This software requires the valection package (http://labs.oicr.on.ca/boutros-lab/software/valection).
There are six selection methods available through six functions. They all take the following arguments:
- **budget**: an integer specifying how many candidates to select
- **infile**: a path to a file which contains the calls from all callers. The infile should be formatted with a tab separating the caller and call on each line:
caller1 name\ta call this caller made caller2 name\ta call this caller made
magnifying glass chr1 576834 magnifying glass chr1 6878924 eye dropper chr1 496267 eye dropper chr1 6878924
Note that the call can contain a tab, but the caller may not.
- **outfile**: a path to a filename where the calls should be outputted
- **seed** (optional): an integer to seed the random number generator with (used to randomize sampling)
use Bio::Sampling::Valection; # Run the sampling to select 10 candidates run_equal_per_caller(10, "/home/me/calls.valec", "/home/me/selections.txt", 50);
The functions are named as follows:
Chris Cooper - Boutros Lab
Paul Boutros, PhD, PI - Boutros Lab
The Ontario Institute for Cancer Research
This software is copyright (c) 2015 by the Ontario Institute for Cancer Research.