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ococo.1
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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
.TH OCOCO "1" "November 2018" "ococo " "User Commands"
.SH NAME
ococo \- Online variant and consensus caller
.SH SYNOPSIS
ococo -i <SAM/BAM file> [other options]
.SH DESCRIPTION
Ococo is a program to call variants and a 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 a 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
Print consensus in FASTA.
.TP
\fB\-S\fR, \fB\-\-stats\-out\fR FILE
Export statistics to a file.
.TP
\fB\-V\fR, \fB\-\-vcf\-cons\fR FILE
Print inferred variants in VCF (\- for standard output).
.TP
\fB\-P\fR, \fB\-\-pileup\fR FILE
Print SAMtools pileup (\- for standard output).
.TP
\fB\-\-verbose\fR
Use the verbose mode (report every update of a counter).
.SS "Parameters for consensus calling:"
.TP
\fB\-x\fR, \fB\-\-counters\fR STR
Counter configuration [ococo32].
.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\-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
Karel Brinda ([email protected]).
.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] Brinda K, Boeva V, Kucherov G.
.B Ococo: an online variant and consensus caller.
arXiv:1712.01146 [q-bio.GN], 2018.