Tool to detect Copy Number Variations(CNV) using Single Read End Data

Question

[gskbioinfo143]

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

Thanks

Answer 1

[Evgeniia Golovina]

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

[gskbioinfo143]

According to this post 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

[Charles Warden]

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).