Question: Tool to detect Copy Number Variations(CNV) using Single Read End Data
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gravatar for gskbioinfo143
3.9 years ago by
India
gskbioinfo14350 wrote:

Hey any one pls list out Accurate detection of CNV using Single Read End Data

Thanks

cnv • 1.9k views
ADD COMMENTlink modified 3.9 years ago by Evgeniia Golovina970 • written 3.9 years ago by gskbioinfo14350
0
gravatar for Evgeniia Golovina
3.9 years ago by
New Zealand
Evgeniia Golovina970 wrote:

Hmm...Detection of copy-number variation is based on read-depth and it doesn't matter whether your data is paired-end or single-end. There are some tools that will call copy number variations:

readDepth

BreakDancer

GASV

PEMer

ADD COMMENTlink written 3.9 years ago by Evgeniia Golovina970

According to this post C: Copy Number Variation (Cnv) Detection Using Single-End Sequencing Data they r tools to detect CNV using single read data

for single read data generated from ion torrent is thre any tool for cnv detection

Thanks

 

ADD REPLYlink written 3.9 years ago by gskbioinfo14350

I think there are a couple caveats:

1) I think BreakDancer might require paired end data.  I seem to remember it needing to be able to reliably determine the insert size

2) I think CoNIFER is a pretty good coverage-based analysis tool (with the right parameter settings, I believe the calls that it makes, but it probably has a lot of false negatives).  However, that is mostly with Illumina data using array-based targeted sequencing.  I believe most targeted Ion Torrent applications use amplicon-based targeted sequencing.  Also, CoNIFER requires a decent number of samples to call rare copy number variants (so, you can't just apply it to 1-3 samples).

ADD REPLYlink written 3.9 years ago by Charles Warden6.1k
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