mutantCaller: Mutant Calling Function for Sanger Sequencing

In jaredbrewer/mutantCall: Automatically calls heterozygous mutants from Sanger sequencing

Description

This function will allow you to automatically call heterozygous mutations from Sanger sequencing

Usage

mutantCaller(test.seq, ref, length, trim5 = 25, trim3 = 25)

Arguments

test.seq	Input the sequence you wish to test (as a string pointing to a file in your working directory).
ref	Input the reference sequencing (you did sequence a control, right?)
length	Input the approximate length of your usable sequence as a positive integer.
trim5	You can manually adjust the amount of trimming done from the 5' end - defaults to 25.
trim3	You can manually adjust the amount of trimming done from the 3' end - defaults to 25.

Examples

mutantCaller(test.seq = './24A_005_JB-T5_JB61_E01.ab1', ref = './24A_001_JB-TM_JB61_A01.ab1', length = 400)
P1               101 ACGACCAGCTCCAGGAGTACGTCCAGCAGACCGTCG--GCCCAGAAACAC    148
                     ||||||||||||||||||||||||||||||||||||  ||||||||||||
S1               101 ACGACCAGCTCCAGGAGTACGTCCAGCAGACCGTCGCAGCCCAGAAACAC    150
This is a two base pair insertion because the secondary sequence is longer than the primary.

jaredbrewer/mutantCall documentation built on May 28, 2019, 11:01 p.m.