ococo.1

.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH OCOCO "1" "August 2016" "ococo " "User Commands"
.SH NAME
ococo \- Online consensus caller
.SH SYNOPSIS
ococo -i <SAM/BAM file> [other options]
.SH DESCRIPTION
Ococo is a program to call genomic consensus directly from an unsorted
SAM/BAM stream.
.SS "Input options:"
.TP
\fB\-i\fR, \fB\-\-input\fR FILE
Input SAM/BAM file (\- for standard input).
.TP
\fB\-f\fR, \fB\-\-fasta\-ref\fR FILE
Initial FASTA reference (otherwise seq of N's is used).
.TP
\fB\-s\fR, \fB\-\-stats\-in\fR FILE
Input statistics.
.SS "Output options:"
.HP
\fB\-F\fR, \fB\-\-fasta\-cons\fR FILE FASTA file with consensus
.TP
\fB\-S\fR, \fB\-\-stats\-out\fR FILE
Output statistics.
.TP
\fB\-V\fR, \fB\-\-vcf\-cons\fR FILE
VCF file with updates of consensus (\- for standard output)
.TP
\fB\-P\fR, \fB\-\-pileup\fR FILE
Truncated pileup (\- for standard output).
.TP
\fB\-\-verbose\fR
Verbose mode (report every update of a counter).
.SS "Parameters for consensus calling:"
.TP
\fB\-x\fR, \fB\-\-counters\fR STR
Counter configuration [ococo16].

.TS
l	l	l	.
.B
configuration	bits/counter	bits/position
ococo16	3	16
ococo32	7	32
ococo64	15	64
.TE

.TP
\fB\-m\fR, \fB\-\-mode\fR STR
Mode [batch].

.TS
l	l	.
.B
mode	description
real\-time	updates reported immediately
batch	updates reported after end of algn stream
.TE

.TP
\fB\-t\fR, \fB\-\-strategy\fR STR
Strategy for updates [majority].

.TS
l	l	l	.
.B
strategy	description
majority	update to majority base
stochastic	update to stochastically drawn base
no-updates	no updates, only counters updated
.TE

.TP
\fB\-q\fR, \fB\-\-min\-MQ\fR INT
Skip alignments with mapping quality smaller than INT [1].
.TP
\fB\-Q\fR, \fB\-\-min\-BQ\fR INT
Skip bases with base quality smaller than INT [13].
.TP
\fB\-w\fR, \fB\-\-ref\-weight\fR INT
Initial counter value for nucleotides from ref [0].
.TP
\fB\-c\fR, \fB\-\-min\-cov\fR INT
Minimum coverage required for update [2].
.TP
\fB\-M\fR, \fB\-\-maj\-thres\fR FLOAT
Majority threshold [0.51].
.SH AUTHOR
Written by Karel Brinda (kbrinda@hsph.harvard.edu).
.SH REPORTING BUGS
Report bugs on https://github.com/karel-brinda/ococo/issues
.SH EXAMPLES
ococo \-i test.bam \-f test.fa \-m real\-time \-V \-

ococo \-x ococo64 \-i test.bam \-f test.fa \-P \- \-V variants.vcf
.SH LICENSE AND CITATION
Ococo is distributed under the MIT license. If you use the program,
please cite the following paper:

[1] K. Brinda, V. Boeva, G. Kucherov.
.B Dynamic read mapping and online consensus calling for better variant detection.
arXiv:1605.09070 [q-bio.GN].