Bio::Pipeline::Comparison::Generate::VCFWriter - Create a VCF with the differences between a reference and a single evolved genome. Outputs a gzipped VCF file and a tabix file.
version 1.123050
Create a VCF with the differences between a reference and a single evolved genome
use Bio::Pipeline::Comparison::Generate::VCFWriter; my $obj = Bio::Pipeline::Comparison::Generate::VCFWriter->new(output_filename => 'my_snps.vcf.gz'); $obj->add_snp(1234, 'C', 'A'); $obj->add_snp(1234, 'T', 'A'); $obj->create_file();
Stage a base position in the reference genome, the reference base and a new base for writing to the VCF file.
Create the VCF file and gzip it. Create an index for the file using tabix.
Optional input parameter. This is the name that goes in the column of the VCF file. The output filename is used as the base for this name by default.
Bio::Pipeline::Comparison
Andrew J. Page <ap13@sanger.ac.uk>
This software is Copyright (c) 2012 by Wellcome Trust Sanger Institute.
This is free software, licensed under:
The GNU General Public License, Version 3, June 2007
To install Bio::Pipeline::Comparison, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Pipeline::Comparison
CPAN shell
perl -MCPAN -e shell install Bio::Pipeline::Comparison
For more information on module installation, please visit the detailed CPAN module installation guide.