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Variant_Identification.md

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##SV Identification

  1. [BreakDancer] (http://gmt.genome.wustl.edu/packages/breakdancer/)
  • Description: Genome wide detection of structural variants; Includes two complementary programs, BreakDancerMini (small indel detection) and BreakDancerMax (5 types of structural variants)
  • Input: Set of map files produced by a front-end aligner (MAQ, BWA, NovoAlign, and Bfast) and a tab-delimited file containing locations of the map files, detection parameters and sample information
  • Output:File containing 14 columns
  1. [Delly2] (https://github.com/tobiasrausch/delly)
  • Description: Can discover and genotype deletions, tandem duplications, inversions and translocations; uses paired-ends and split-reads; SVs can be visualized using Delly-maze and Delly-sauve
  • Input: Bam
  • Output: VCF
  1. [Genome STRiP] (http://www.broadinstitute.org/software/genomestrip/)
  • Description: Set of tools for structural variant identification and genotyping; requires genomes from multiple individuals (20-30 minimum); Uses GATK and consists of multiple modules
  • Input: BAM
  • Output: VCF
  1. [mrFast] (http://mrfast.sourceforge.net/)
  • Description: micro-read Fast Alignment Search Tool; designed to map short reads generate with Illumina
  • Input:
  • Output: SAM
  1. [mrsFast] (http://sfu-compbio.github.io/mrsfast/)
  • Description: Micro-read substitution-only Fast Alignment Search Tool; designed to map short reads to reference genome assemblies
  • Input: FastQ *Reference Genome: FASTA
  • Output: SAM
  1. [NovelSeq] (http://novelseq.sourceforge.net)
  • Description: Designed to detect novel sequence insertions using high-throughput paired-end whole genome sequencing data
  • Input: FASTA or FASTQ
  • Output: FASTA file containing paired-end sequences
  1. [PEMer] (http://sv.gersteinlab.org/pemer/)
  • Description: Command line package composed of three modules (PEMer workflow, SV-Simulation, and BreakDB) for SV analysis
  • Input: FASTA
  • Output:
  1. [Pindel] (http://gmt.genome.wustl.edu/packages/pindel/)
  • Description: Command line package program for detection of “large deletions, medium sized insertions, inversions, tandem duplications, and other structural variations”
  • Input: SAM/BAM
  • Output: pindel raw output format (can be converted to VCF)
  1. [SVMerge] (http://svmerge.sourceforge.net/)
  • Description: Pipeline for detecting structural variants by integrating calls from different SV callers
  • Input: BAM
  • Output: multiple (depends on SV callers used)
  1. [TIGRA] (http://bioinformatics.mdanderson.org/main/TIGRA)
  • Description: Command line package program that “conducts targeted local assembly of structural variants using targeted iterative graph routing assembly algorithm” Uses data from 1000 Genomes project
  • Input: SV file; group of BAM files
  • Output: Fasta