It is really hard to say that which is the better tool for In-Del identification. It is always better to go for more than one algorithm to detect In-Dels. And one also should not expect complete overlap of results obtained using different softwares, because each software has its own model to call variants. I am a fan of GATK HaplotypeCaller because of several reasons, like building haplotype for each In-Dels and context dependent model for calling variants. Mpileup and freebayes are also a quite famous among researchers. So rather I would suggest you to take any of these as a base algorithm to call In-Dels. Obviously overlapping In-Dels will be the ones with high confidence and non-overlapping In-Dels can be confirmed/discarded after doing sanger sequencing.

Good Luck

Hi,

as said by Sourav, it's really complex to find out the best variant caller. I suggest to take a look to this publication, it will surely help you:

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0075619

Have you checked out BreakDancer?

Hi, Please check out this link:

I wish you will find somthing

http://www.oxfordjournals.org/our_journals/bioinformatics/nextgenerationsequencing.html

I use splitread designed by a postdoc from Evan Eichler's lab, tested on WGS and exome sequencing data:

http://splitread.sourceforge.net/

Speaking of INDEL callers, Scalpel was extensively benchmarked in this below paper, showing high accuracy (especially for large indels).

Accurate de novo and transmitted indel detection in exome-capture data using microassembly

Also, we highlighted the use of Scalpel to reduce errors in whole-genome and whole-exome studies in a follow-up paper.

Reducing INDEL calling errors in whole genome and exome sequencing data

Scalpel is available here: http://scalpel.sourceforge.net/

http://www.nature.com/nmeth/journal/v11/n10/full/nmeth.3069.html

http://genomemedicine.com/content/6/10/89/

http://scalpel.sourceforge.net/