Question

NGS CNVtools with no controls

1

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9.5 years ago

hellbio ▴ 520

Hi,

There are a lot of NGS tools to detect CNVs from exome and whole genome sequencing data. However, most of the tools which I came across do need a control to calculate the CNVs. Could someone suggest some good tools which can work without control sample.

ngs cnv • 2.5k views

ADD COMMENT • link updated 2.2 years ago by Ram 43k • written 9.5 years ago by hellbio ▴ 520

Ram · Answer 1 · 2014-11-09

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9.5 years ago

Zev.Kronenberg 12k

WaveCNV doesn't require a control. It also creates some very nice figures automatically.

http://www.ncbi.nlm.nih.gov/pubmed/24192544

ADD COMMENT • link updated 2.2 years ago by Ram 43k • written 9.5 years ago by Zev.Kronenberg 12k

Ram · Answer 2 · 2014-11-09

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9.5 years ago

poisonAlien ★ 3.2k

cn.mops would do this with low FDR.

ADD COMMENT • link updated 2.2 years ago by Ram 43k • written 9.5 years ago by poisonAlien ★ 3.2k

score 0 · Answer 3 · 2014-11-10

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9.5 years ago

Fedor Gusev ▴ 210

FREEC can do that. http://bioinfo-out.curie.fr/projects/freec/

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