Bug#818605: ITP: dindel -- find insertions and deletions in biological sequences

["Steffen Möller" <steffen_moeller@gmx.de>]

Package: wnpp
Severity: wishlist
Owner: Steffen Moeller <steffen_moeller@gmx.de>
 
* Package name    : dindel
* URL             : https://sites.google.com/site/keesalbers/soft/dindel
* License         : GPL-3.0+
  Description     : find insertions and deletions in biological sequences

 The packaging is ready and about to surface on the Debian Med git repository.

 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.