.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH COVTOBED "1" "September 2020" "covtobed 1.1.4" "User Commands"
.SH NAME
covtobed \- convert the coverage track from a BAM file into a BED file
.SH SYNOPSIS
.B covtobed
[\fI\,options\/\fR] [\fI\,BAM\/\fR]...
.SH DESCRIPTION
Computes coverage from alignments
.SH OPTIONS
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-\-physical\-coverage\fR
compute physical coverage (needs paired alignments in input)
.TP
\fB\-q\fR MINQ, \fB\-\-min\-mapq\fR=\fI\,MINQ\/\fR
skip alignments whose mapping quality is less than MINQ
(default: 0)
.TP
\fB\-m\fR MINCOV, \fB\-\-min\-cov\fR=\fI\,MINCOV\/\fR
print BED feature only if the coverage is bigger than
(or equal to) MINCOV (default: 0)
.TP
\fB\-x\fR MAXCOV, \fB\-\-max\-cov\fR=\fI\,MAXCOV\/\fR
print BED feature only if the coverage is lower than
MAXCOV (default: 100000)
.TP
\fB\-l\fR MINLEN, \fB\-\-min\-len\fR=\fI\,MINLEN\/\fR
print BED feature only if its length is bigger (or equal
to) than MINLELN (default: 1)
.TP
\fB\-d\fR, \fB\-\-discard\-invalid\-alignments\fR
skip duplicates, failed QC, and non primary alignment,
minq>0 (or user\-defined if higher) (default: 0)
.TP
\fB\-\-output\-strands\fR
output coverage and stats separately for each strand
.TP
\fB\-\-format\fR=\fI\,CHOICE\/\fR
output format