Entering edit mode
4.2 years ago
prameelaawale
•
0
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.
Please read the manual: https://github.com/arq5x/lumpy-sv