.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH LUMPYEXPRESS "1" "June 2020" "lumpyexpress 0.3.0" "User Commands"
.SH NAME
lumpyexpress \- Automated breakpoint detection for standard analyses
.SH SYNOPSIS
.B lumpyexpress
[options]
.SH OPTIONS
.TP
\fB\-B\fR FILE
full BAM or CRAM file(s) (comma separated) (required)
.TP
\fB\-S\fR FILE
split reads BAM file(s) (comma separated)
.TP
\fB\-D\fR FILE
discordant reads BAM files(s) (comma separated)
.TP
\fB\-R\fR FILE
indexed reference genome fasta file (recommended for CRAMs)
.TP
\fB\-d\fR FILE
bedpe file of depths (comma separated and prefixed by sample:)
e.g sample_x:/path/to/sample_x.bedpe,sample_y:/path/to/sample_y.bedpe
.TP
\fB\-o\fR FILE
output file [fullBam.bam.vcf]
.TP
\fB\-x\fR FILE
BED file to exclude
.TP
\fB\-P\fR
output probability curves for each variant
.TP
\fB\-m\fR INT
minimum sample weight for a call [4]
.HP
\fB\-r\fR FLOAT trim threshold [0]
.TP
\fB\-T\fR DIR
temp directory [./output_prefix.XXXXXXXXXXXX]
.TP
\fB\-k\fR
keep temporary files
.TP
\fB\-K\fR FILE
path to lumpyexpress.config file
.IP
(default: same directory as lumpyexpress)
.TP
\fB\-v\fR
verbose
.TP
\fB\-h\fR
show this message
.PP
Error: \fB\-B\fR is required
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.