dindel_1.01+dfsg-4build2_amd64.deb


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Description

dindel - determines indel calls from short-read data

Property Value
Distribution Ubuntu 18.04 LTS (Bionic Beaver)
Repository Ubuntu Universe amd64
Package name dindel
Package version 1.01+dfsg
Package release 4build2
Package architecture amd64
Package type deb
Installed size 921 B
Download size 328.11 KB
Official Mirror archive.ubuntu.com
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.

Alternatives

Package Version Architecture Repository
dindel_1.01+dfsg-4build2_i386.deb 1.01+dfsg i386 Ubuntu Universe
dindel - - -

Requires

Name Value
libboost-program-options1.65.1 -
libc6 >= 2.15
libgcc1 >= 1:3.0
libstdc++6 >= 5.2
zlib1g >= 1:1.2.3.3

Download

Type URL
Binary Package dindel_1.01+dfsg-4build2_amd64.deb
Source Package dindel

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install dindel deb package:
    # sudo apt-get install dindel

Files

Path
/usr/bin/dindel
/usr/share/doc/dindel/README
/usr/share/doc/dindel/changelog.Debian.gz
/usr/share/doc/dindel/copyright
/usr/share/man/man1/dindel.1.gz

Changelog

2017-10-26 - Matthias Klose <doko@ubuntu.com>
dindel (1.01+dfsg-4build2) bionic; urgency=medium
* No-change rebuild for boost soname change.
2016-11-01 - Dimitri John Ledkov <xnox@ubuntu.com>
dindel (1.01+dfsg-4build1) zesty; urgency=high
* No change rebuild against boost1.62.
2016-08-10 - Sascha Steinbiss <satta@debian.org>
dindel (1.01+dfsg-4) unstable; urgency=medium
* Team upload.
* Make code compatible with latest Boost version (1.61 and up).
Thanks to Graham Inggs for the patch.
Closes: #833958
2016-08-06 - Sascha Steinbiss <satta@debian.org>
dindel (1.01+dfsg-3) unstable; urgency=medium
* Team upload.
* Force use of Boost 1.58 to fix FTBFS with newer Boost versions.
* Bump Standards-Version.
* d/copyright: Reorder items.
* d/copyright: Use secure Format URL.
2016-08-03 - Sascha Steinbiss <satta@debian.org>
dindel (1.01+dfsg-2) unstable; urgency=medium
* Team upload.
* Fix FTBFS with GCC 6.
Closes: #831208
2016-03-18 - Animesh Sharma <sharma.animesh@gmail.com>
dindel (1.01+dfsg-1) unstable; urgency=low
* Initial release (Closes: #818605)

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