[Debian-med-packaging] Bug#861664: ITP: manta -- structural variant and indel caller for mapped sequencing data

Andreas Tille tille at debian.org
Tue May 2 12:38:47 UTC 2017

Package: wnpp
Severity: wishlist
Owner: Andreas Tille <tille at debian.org>

* Package name    : manta
  Version         : 1.1.0
  Upstream Author : Illumina, Inc.
* URL             : https://github.com/Illumina/manta
* License         : GPL
  Programming Lang: C++, Python
  Description     : structural variant and indel caller for mapped sequencing data
 Manta calls structural variants (SVs) and indels from mapped paired-end
 sequencing reads. It is optimized for analysis of germline variation in
 small sets of individuals and somatic variation in tumor/normal sample
 pairs. Manta discovers, assembles and scores large-scale SVs, medium-
 sized indels and large insertions within a single efficient workflow.
 The method is designed for rapid analysis on standard compute hardware:
 NA12878 at 50x genomic coverage is analyzed in less than 20 minutes on a
 20 core server, and most WGS tumor/normal analyses can be completed
 within 2 hours. Manta combines paired and split-read evidence during SV
 discovery and scoring to improve accuracy, but does not require split-
 reads or successful breakpoint assemblies to report a variant in cases
 where there is strong evidence otherwise. It provides scoring models for
 germline variants in small sets of diploid samples and somatic variants
 in matched tumor/normal sample pairs. There is experimental support for
 analysis of unmatched tumor samples as well. Manta accepts input read
 mappings from BAM or CRAM files and reports all SV and indel inferences
 in VCF 4.1 format.

Remark: This package will be maintained by the Debian Med team at

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