Question: Insertion Detection Tools
0
gravatar for lyfsa
8.0 years ago by
lyfsa30
lyfsa30 wrote:

Hi,

Please suggest me some tools which can detect large indels (esp. of size > 100bp). Some of the tools I have already tried include Breakdancer and Pindel and Hydra. Any other suggestions??

indel tool • 2.9k views
ADD COMMENTlink written 8.0 years ago by lyfsa30
5
gravatar for VS
8.0 years ago by
VS710
USA
VS710 wrote:

I presume you mean tools for NGS data. There are lots -- You can try CNV-seq, exomecopy, CNVnator, BIC-Seq and cn.MOPS

ADD COMMENTlink written 8.0 years ago by VS710
4
gravatar for Irsan
8.0 years ago by
Irsan7.2k
Amsterdam
Irsan7.2k wrote:

See http://www.gen2phen.org/wiki/tools-and-methods-mapping-genomic-structural-variation (see bottom page for suggestions)

I would recommend delly as well (is not in that list):

http://www.embl.de/~rausch/delly.html

ADD COMMENTlink written 8.0 years ago by Irsan7.2k
3
gravatar for zam.iqbal.genome
8.0 years ago by
United Kingdom
zam.iqbal.genome1.7k wrote:

Assembly is the best way to access insertions. Various approaches, either

  1. Global variant assembly. Here's the paper where this approach is introduced:

"De novo assembly and genotyping of variants using colored de Bruijn graphs." Z Iqbal, M Caccamo, I Turner, P Flicek, G McVean, Nature Genetics (2012)

a)Cortex will do this http://cortexassembler.sourceforge.net/index_cortex_var.html

b) So will SGA https://github.com/jts/sga

  1. Local assembly by taking reads from a bam

a) There are versions of these using SGA and Cortex (the latter is called Platypus) being used in the 1000 Genomes project, you could ask Jared Simpson at the Sanger Institute or Gerton Lunter at the Wellcome Trust Centre for Human Genetics in Oxford about those. Both of these show a lot of promise.

b) Brad Chapman at EdgeBio has incorporated local Cortex assembly into CloudBioLinux http://bcbio.wordpress.com

c) The Broad have recently started providing local de novo assembly in GATK, but not sure it will do many >100bp calls.

cheers

Zam

ADD COMMENTlink written 8.0 years ago by zam.iqbal.genome1.7k

Also, you could try NovelSeq http://bioinformatics.oxfordjournals.org/content/26/10/1277.full

ADD REPLYlink written 8.0 years ago by zam.iqbal.genome1.7k
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