Question: CNV analysis from a family of 4 exome sequences
0
gravatar for jknmimi
5.4 years ago by
jknmimi0
United States
jknmimi0 wrote:

I am a high school student finishing an exome sequencing project of a family of 4. I have been able to find lots of SNP data, but not CNV.  I think there may be CNV's in one sample.  Unfortunately I have not been able to use the software tools as my computer skills are pretty weak. Is there a site where I can upload my exome data and have it analyzed?  Free or cheap?  Thank you, this is a great website.

sequencing snp cnv • 2.1k views
ADD COMMENTlink modified 5.4 years ago by Daniel Swan13k • written 5.4 years ago by jknmimi0

Sorry could you clarify .. you say " have been able to find lots of SNP data, but not CNV" but then also that you seem to already have all the data.

So is what you mean that you want to find tools that people use to analyze CNV information??

ADD REPLYlink written 5.4 years ago by vlaufer260

Please keep comments on the questions constrained to the comments section and not the answer section - thanks!

ADD REPLYlink written 5.4 years ago by Daniel Swan13k

Thank you for your question. Sorry if I am not using the correct terms.   My data arrived with basic summary software that shows SNP's, INDELS of 1-6 bases.  What I'm trying to find are larger regions of insertions or deletions.  My thinking is that if one of my samples has a large deletion/insertion I can compare it to the other 3 samples (where the deletion/insertion may not exist).  I have the raw data too, but need (easy to use) tools to compare the 4 family samples.  Thank you.

ADD REPLYlink written 5.4 years ago by jknmimi0
1

It would help if you could clarify what data has been returned to you - Fastq files, BAM files, VCF files, annotation files (with gene names in etc.).  Most CNV software requires BAM files, but as this is a a fairly complex procedure you will probably not have great success in finding free 'point and click' tools for it.

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by Daniel Swan13k

Thank you for your help!  I have FASTQ files and can export SAM,BAM and can get VCF in beta.  Yes I have annotated files with gene names, position, type of variant (stop gain, stop loss, etc) ref. and variant, rs#'s, Everything I have seen for CNV software is really complex and that's probably why I haven't found any "point and click" tools. 

I put all of the variants into Excel and can see regions where the one sample shows nothing at all, and the other 3 (parents and sibling)  have lots of variants.  Do you know if this is what a CNV deletion might look like?  Or just a sequencing error?

Any ideas very much appreciated.

 

ADD REPLYlink written 5.4 years ago by jknmimi0

The problem with exome data, is it's hard to tell (by eye) what is 'missing' in a sample because it is not there in the DNA, and where the exome capture process is variable between samples - this is the essence of the complexity of CNV detection in exome studies.  I do think that VarScan2 might be your best bet, because it's written in Java and wont involve you getting stuck trying to learn R to get going.  However, you're going to have to get grips with the command line tools whatever you do..

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by Daniel Swan13k

Thank you so much!

ADD REPLYlink written 5.4 years ago by jknmimi0
2
gravatar for Daniel Swan
5.4 years ago by
Daniel Swan13k
Aberdeen, UK
Daniel Swan13k wrote:

There are previous discussions on CNV analysis of exome data on the site:

What Are The 'Copy Number Detection' Tools Out There For Exome Capture Ngs Data. 

Best Copy Number Variation Tools

Manipulating Normal Individual Data For Cnv Analysis

ADD COMMENTlink written 5.4 years ago by Daniel Swan13k
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