Ion Torrent Data, Aligners & Variant Detection

Venu Thatikonda

Sequencing platforms

SOLiD

Sample Sequence dataIon Torrent Sequencer

FastQ(SFF)

FastQ Format

General Workflow

Sequence data

Alignment / Mapping of short reads to Reference Sequence

Variant detection(SNPs, InDels)

Alignment / MappingWhy it is important ?

* Easiest way to find genetic variations in a sample

What are the problems ?•Short reads don’t contain position information•Reference sequence might be very long – computationally demanding•Ref. Seq might contain several places for a single read (Ex: Repetitive regions)•Allow mismatches during alignment•Instrument might produce sequence errors that are similar to real genetic variations

Aligners/Mappers

Bowtie2

BWA-SW

CLC Mapper

CUSHAW3

GMAP

GSNAP

Hpg-Aligner

Novoalign

NextGenMap

OSA

segemehl

SMALT

STAR

MOSAIK

SNAP TMAP

Choosing best mapper

•No one point solution for all applications arised from HTS•Depends on the instrument used and application

Efficient detection of Mutation – TMAP Bowtie2 SHRIMP2 SSAHA2 Segmehl

SMALT – deals with repeat regions

Variant Detection

Tools used for Variant Detection

GATKGATK - UnifiedGenotyper

GATK - HaplotypeCaller

VarScanpileup2SNP

pileup2InDel

FreeBayes, MAQ, samtools, SOAPsnp, SNVmix, VariantHunter etc.

VarScan – Conserved parameters

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Thank you !