mgymrek/lobstr-code — pull request #29 by tfwillems (2014-03-12 19:52:20+00:00)
Title: Alignment Checks

Added a series of options to filter reads used for allelotyping.

The option --min-border takes one argument and requires that aligned reads extend past the STR boundaries by a certain number of bp. For users that want to use partially spanning reads, they can specify a large negative number that essentially ignores this option. By default, lobSTR uses a value of 0, which requires that the alignment extend to the STR boundaries.

The option --min-bp-before-indel takes one argument and requires that aligned reads not have an indel within the first N bp from each end of the read. The idea behind this option is that indels near the ends of reads are unlikely to be reliable as they have sufficient flanking sequence to anchor them. By default, lobSTR uses a value of 0 and thus no reads are automatically removed.

The option --min-read-end-match takes one argument and requires that aligned reads perfectly match the reference for the first N bp from each end of the read. This option can be used to ensure that reads are accurately anchored. By default, lobSTR uses a value of 0 and thus no reads are automatically removed.