lumpyexpress - Automated breakpoint detection for standard analyses

        This manpage was written by Andreas Tille for the Debian distribution and
        can be used for any other usage of the program.

lumpyexpress 0.3.0                                  June 2020                                    LUMPYEXPRESS(1)

       lumpyexpress - Automated breakpoint detection for standard analyses

-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

lumpyexpress [options]