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control.dat
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control.dat
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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.S1_LGL_MP = 8000 # (see notes, Jun/20/2016)
stdevInsert.S1_LGL_MP = 1000
minInsertLen.S1_LGL_MP = 300
maxInsertLen.S1_LGL_MP = 30000
avgInsertLen.S2_LGL_MP = 8000
stdevInsert.S2_LGL_MP = 1000
minInsertLen.S2_LGL_MP = 300
maxInsertLen.S2_LGL_MP = 30000
avgInsertLen.S3_LGL_MP = 8000
stdevInsert.S3_LGL_MP = 1000
minInsertLen.S3_LGL_MP = 300
maxInsertLen.S3_LGL_MP = 30000
avgInsertLen.S4_LGL_MP = 8000
stdevInsert.S4_LGL_MP = 1000
minInsertLen.S4_LGL_MP = 300
maxInsertLen.S4_LGL_MP = 30000
avgInsertLen.S5_LGL_MP = 8000
stdevInsert.S5_LGL_MP = 1000
minInsertLen.S5_LGL_MP = 300
maxInsertLen.S5_LGL_MP = 30000
avgInsertLen.S6_LGL_MP = 8000
stdevInsert.S6_LGL_MP = 1000
minInsertLen.S6_LGL_MP = 300
maxInsertLen.S6_LGL_MP = 30000
avgInsertLen.S7_LGL_MP = 8000
stdevInsert.S7_LGL_MP = 1000
minInsertLen.S7_LGL_MP = 300
maxInsertLen.S7_LGL_MP = 30000
avgInsertLen.S8_LGL_MP = 8000
stdevInsert.S8_LGL_MP = 1000
minInsertLen.S8_LGL_MP = 300
maxInsertLen.S8_LGL_MP = 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.S1_LGL_MP = 8000
broken_mates_dense.minLength.S2_LGL_MP = 8000
broken_mates_dense.minLength.S3_LGL_MP = 8000
broken_mates_dense.minLength.S4_LGL_MP = 8000
broken_mates_dense.minLength.S5_LGL_MP = 8000
broken_mates_dense.minLength.S6_LGL_MP = 8000
broken_mates_dense.minLength.S7_LGL_MP = 8000
broken_mates_dense.minLength.S8_LGL_MP = 8000
broken_mates_dense.density = 95.0 # (percentile)
broken_mates_dense.samplingStep = 25
discordant_mates_dense.minLength.S1_LGL_MP = 8000
discordant_mates_dense.minLength.S2_LGL_MP = 8000
discordant_mates_dense.minLength.S3_LGL_MP = 8000
discordant_mates_dense.minLength.S4_LGL_MP = 8000
discordant_mates_dense.minLength.S5_LGL_MP = 8000
discordant_mates_dense.minLength.S6_LGL_MP = 8000
discordant_mates_dense.minLength.S7_LGL_MP = 8000
discordant_mates_dense.minLength.S8_LGL_MP = 8000
discordant_mates_dense.density = 95.0 # (percentile)
discordant_mates_dense.samplingStep = 25
call_insertions.closure = 2K
call_insertions.proximity = 2K