jaudoux/tami

Targeted mutation identification

TaMI : Targeted Mutation Identification

TaMI, is a k-mer base variant caller that directly scan raw FASTQ files and looks for variants without alignement by using a dictionnary of mutated k-mers constructed for specific targets.

TaMI looks for all possible single nucleotide mutations (1-nt indels as well) only on the targeted regions. TaMI is very fast, a whole human exome can be scan within a minute in a single thread. TaMI memory load depend on the size of the indexed target regions.

Installation

• Clone tami repositiory
• run make to compile tami
• place the tami binary somewhere accessible from your $PATH.

Usage

First you need to create a TAM files, wich is a dictionnary of mutated k-mers composed of all possible mutation in the targets (bed file).

tami build -r reference.fasta -o file.tam file.bed

Then you need to scan FASTQ files to look for mutations indexed in the TAM.

tami scan file.tam reads_1.fastq.gz reads_2.fastq.gz > output.vcf

Authors

Jérôme Audoux, Alexandre Soriano.