## Help needed to run Lumpy with pair end discordant reads

Question

[prameelaawale]

Hello everyone. I am trying to use this code below to run Lumpy for pair end discordant file.

  -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>

Can anyone please help me with idea how to determine minimum non overlap, discordant Z value, back distance, min mapping threshold, weight and read group. I do not understand what these means and therefore have no idea what numbers to put on them. Thank you in advance.

[ATpoint]

Please read the manual: https://github.com/arq5x/lumpy-sv