control.dat

clipThreshold                              = 0.10   # this eliminates short unmapped ends

clipped_breakpoints.windowSize             = 10

clipped_breakpoints_high.threshold         = 96.2   # (percentile)
clipped_breakpoints_high.tiesAbove         = 1
clipped_breakpoints_high.samplingStep      = 25

avgInsertLen.*                             = 8000
stdevInsert.*                              = 1000
minInsertLen.*                             = 300
maxInsertLen.*                             = 30000

insert_depth_dense.minLength               = 1000
insert_depth_dense.density                 = 90.0   # (percentile)
insert_depth_dense.densityClip             = 92.0   # (percentile)
insert_depth_dense.samplingStep            = 25

insert_depth_sparse.maskLevel              = 60.0   # (percentile)
insert_depth_sparse.windowLength           = 1000
insert_depth_sparse.minLength              = 500
insert_depth_sparse.density                = 10.0   # (percentile)
insert_depth_sparse.samplingStep           = 25

insert_length_sparse.maskLevel             = 60.0   # (percentile)
insert_length_sparse.windowLength          = 1000
insert_length_sparse.minLength             = 500
insert_length_sparse.density               = 5.0    # (percentile)
insert_length_sparse.densityClip           = 3.0    # (percentile)
insert_length_sparse.samplingStep          = 25

broken_mates_dense.minLength.*             = 8000
broken_mates_dense.density                 = 95.0   # (percentile)
broken_mates_dense.samplingStep            = 25

discordant_mates_dense.minLength.*         = 8000
discordant_mates_dense.density             = 95.0   # (percentile)
discordant_mates_dense.samplingStep        = 25

call_insertions.closure                    = 2K
call_insertions.proximity                  = 2K