NAME
lumpyexpress - Automated breakpoint detection for standard analyses
SYNOPSIS
lumpyexpress [options]
OPTIONS
- -B FILE
-
full BAM or CRAM file(s) (comma separated) (required)
- -S FILE
-
split reads BAM file(s) (comma separated)
- -D FILE
-
discordant reads BAM files(s) (comma separated)
- -R FILE
-
indexed reference genome fasta file (recommended for CRAMs)
- -d 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
- -o FILE
-
output file [fullBam.bam.vcf]
- -x FILE
-
BED file to exclude
- -P
-
output probability curves for each variant
- -m INT
-
minimum sample weight for a call [4]
-r FLOAT trim threshold [0]
- -T DIR
-
temp directory [./output_prefix.XXXXXXXXXXXX]
- -k
-
keep temporary files
- -K FILE
-
path to lumpyexpress.config file
-
(default: same directory as lumpyexpress)
- -v
-
verbose
- -h
-
show this message
Error: -B is required
AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.