NAME

       lumpy - Automated breakpoint detection for standard analyses

SYNOPSIS

       lumpy [OPTIONS]

DESCRIPTION

       LUMPY,  a  novel  SV  discovery  framework  that  naturally integrates multiple SV signals
       jointly across multiple samples.  LUMPY yields improved sensitivity,  especially  when  SV
       signal  is  reduced  owing  to either low coverage data or low intra-sample variant allele
       frequency.

OPTIONS

       -g     Genome file (defines chromosome order)

       -e     Show evidence for each call

       -w     File read windows size (default 1000000)

       -mw    minimum weight for a call

       -msw   minimum per-sample weight for a call

       -tt    trim threshold

       -x     exclude file bed file

       -t     temp file prefix, must be to a writeable directory

       -P     output probability curve for each variant

       -b     output BEDPE instead of VCF

       -sr    bam_file:<file name>,

              id:<sample name>,

              back_distance:<distance>,

              min_mapping_threshold:<mapping quality>,

              weight:<sample weight>,

              min_clip:<minimum clip length>,

              read_group:<string>

       -pe    bam_file:<file name>,

              id:<sample name>,

              histo_file:<file name>,

              mean:<value>,

              stdev:<value>,

              read_length:<length>,

              min_non_overlap:<length>,

              discordant_z:<z value>,

              back_distance:<distance>,

              min_mapping_threshold:<mapping quality>,

              weight:<sample weight>,

              read_group:<string>

       -bedpe bedpe_file:<bedpe file>,

              id:<sample name>, weight:<sample weight>

AUTHOR

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