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Dindel


Dindel is a program for calling small indels from short-read sequence data ('next generation sequence data'). It currently is designed to handle only Illumina data.

Dindel requires a BAM file containing the read-alignments as input. It then extracts candidate indels from the BAM file, and realigns the reads to candidate haplotypes consisting of these candidate indels. If there is sufficient evidence for an alternative haplotype to the reference, it will call an indel.

It is possible to test indels discovered with other methods using Dindel, for instance longer indels obtained through assembly methods. Dindel will then realign both mapped and unmapped reads to see if the candidate indel is supported by the reads.

Dindel outputs both genotype likelihoods and includes a script to convert these to a VCF file with indel and SNP calls.

There is basic support for outputting realigned BAM files for each realignment-window. These realigned BAM files can be used to call SNPs near (candidate) indels. See the manual for details.

29 October 2010

The new version of Dindel 1.01 fixes a number of small bugs and the updated Python scripts now produce VCF4 files with the indel calls. It also includes a script to convert VCF4 indels to candidates that can be tested with Dindel. See the manual for details.

Publication

The Dindel paper is described in the following publication:

Dindel: Accurate indel calls from short-read data
  • Cornelis A. Albers
  • Gerton Lunter
  • Daniel G. MacArthur
  • Gilean McVean,
  • Willem H. Ouwehand
  • and Richard Durbin
http://genome.cshlp.org/content/early/2010/10/25/gr.112326.110.abstract

Please note that this is not the final version and that there is an error in table 2. The number of indels for Dindel should be 588 and the number of indels for VarScan (q10) should be 534 in the second column under 'Indels called'.

Dindel was used to make the low-coverage pilot and trio pilot indel call sets for the 1000 Genomes Project. The 1000 Genomes paper is here:

Note

The current version of Dindel is 1.01. Please let me know if you have any problems or suggestions for improving Dindel or the manual, by sending an email to

caa (at) sanger.ac.uk

Download

Version 1.01

Released 28th October 2010. This version fixes a number of small bugs and has some additional scripts to facilitate the analysis. Dindel now also produces calls in the VCF4 format. The source code is now also available.

Version 0.12

Released 14th June 2010. Added support for analysis of pools.

Version 0.11

Released 6th  May  2010. Go to the bottom of this page to download the software.
Fixed a bug in the makeWindows.py script.

Version 0.1

Released 9th  April  2010. Go to the bottom of this page to download the software.
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dindel-0.12.tar.gz
(1229k)
Kees Albers,
14 Jun 2010, 07:34
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dindel-1.01-linux.tar.gz
(1157k)
Kees Albers,
28 Oct 2010, 01:38
ċ
dindel-1.01-max-os-x.tar.gz
(458k)
Kees Albers,
28 Oct 2010, 01:37
ċ
dindel-1.01-src.tar.gz
(1387k)
Kees Albers,
28 Oct 2010, 01:37
Ċ
Kees Albers,
14 Jun 2010, 07:34
Ċ
Kees Albers,
28 Oct 2010, 01:37
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