Description Usage Arguments Details Value Author(s)
For repeats that have read pairs flanking them, the implied expansion and length of that repeat is determined.
1 2 3 | calculateIRLs_MLE(flanking_file, imd_distribution,
upper_limit = 0.95, margin = 37.5, min_coverage = 10,
output_dir)
|
flanking_file |
_flanking read pair file |
imd_distribution |
.insert_len_dist file (i.e. the inner mate distance distribution for the sample) |
upper_limit |
the value used in mapATR processLastAlignedBase [default= 0.95] |
margin |
the value used in mapATR processLastAlignedBase [default= 37.5] |
min_coverage |
minimum number of flanking read pairs that map to a given repeat required for IRL calculation [default= 10] |
output_dir |
path to output directory |
Summary stats for the implied repeat exansions/lengths are also reported.
_implied_repeat_lengths file
Adam Struck - Intern
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