Question

Detecting CNVs from BAM file

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3.3 years ago

DKA ▴ 40

Hello everyone, Are there any tools or software or any websites that can detect CNVs (Copy number variants) from BAM file, which are designed for people who do not have any experience in coding or programming, please? Thank you

sequencing genome • 835 views

ADD COMMENT • link 3.3 years ago by DKA ▴ 40

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what did you find so far ?

ADD REPLY • link 3.3 years ago by Pierre Lindenbaum 161k

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Unfortunately, nothing.

ADD REPLY • link 3.3 years ago by DKA ▴ 40

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Control-FREEC (shell)
DNAcopy (R)

ADD REPLY • link 3.3 years ago by Kevin Blighe 87k

score 3 · Answer 1 · 2020-12-26

Hi,

At the least if you have a test and a control sample (BAM), then you can try Galaxy. Its a website with all sorts of tools for genomic data manipulation, but without needing to use programming/ command-line tools. You would need to upload your files there, of course. There is sufficient documentation available for you to get going. An important point to keep in mind is that not every tool available for a given task would be available. For comparatively common tasks more tools are available, as compared to more niche areas. Having said that, a quick search tells me that ExomeDepth is available. If you are ready to invest some time, then this can get you started.