findStutter: Find locus specific stutter given motif.

In romunov/fishbone: Tools for Calling Alleles/Genotypes from Illumina NGS Sequences

Description

Try to find a stutter. It will try its best to find a stutter no matter where in the sequence the motif may be missing.

Usage

findStutter(x, fb, motif)

Arguments

x	A fishbone object.
fb	A fishbone object with candidate stutter alleles.
motif	Character. Motif of the repeat.

Details

Algorithm:

• 1. count number of motif repeats in a sequence

• 2. count number of motif repeats in reverse of sequence

• 3. if no motif repeats, signal that motif was not found

• 4. find locations of all motif occurrences

• 5. for each direction of sequence and for every location...

• 5a. shorted candidate sequence

• 5b. compare shortened sequence to possible stutter candidates

• 5c. if found, signal stutter found and exit

• 5d. if not found, remove second occurrence and compare to stutter candidates

• 5e. repeat 3-3d until all positions tested

• 6a. if match not found, declare no stutter found

Value

A character string of stutter(s) ID. If stutter is not found, it returns NULL.

Author(s)

Roman Lustrik ([email protected])

romunov/fishbone documentation built on Nov. 3, 2018, 8:28 p.m.