bam2consensus - consensus calling (etc) from BAM alignment
bam2consensus --bam <in.bam> --ref <in.fasta> [options] --consensus <out.fasta>
Re-calls a consensus sequence based on a BAM alignment to reference, with various knobs and optional output formats
Requires the following non-core Perl libraries:
as well as the following binaries:
Path to input BAM alignments
Path to reference sequence used to generate BAM alignments
Path to write consensus sequence to (as FASTA)
Path to write coverage file to (as bedgraph)
Path to write coverage file to (as tab-separated table)
Minimum quality for a base to be considered in consensus calling. Default: 10.
Minimum read depth for consensus to be called (otherwise called as "N"). Default: 3.
Fraction to trim from each end when calculating trimmed mean of error window. Default: 0.2.
Size of sliding window used to calculate local error rates. Default: 30.
If greater than zero, the number of significant figures used to bin depths in bedgraph output. If zero, no binning is applied. This option is useful to reduce the size of bedgraph output by binning similar depth values when high resolution is not important. Default: 0 (disabled).
Please submit bug reports to the issue tracker in the distribution repository.
Jeremy Volkening (jeremy.volkening@base2bio.com)
Copyright 2014-23 Jeremy Volkening
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.