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.