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

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

Thanks

cnv
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updated by Ram Ram • written by gskbioinfo143 • gskbioinfo143

1 answer

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:

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updated by Ram Ram • written by Evgeniia Golovina Evgeniia Golovina

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).
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updated by Ram Ram • written by Charles Warden Charles Warden

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