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.