Analyzing data with bioscope

elondin · 01-20-2011, 12:12 PM

Hi all,
I am in the midst of doing my first exome sequencing data analyis project. The experiment involved paired-end sequencing and am starting to analyze the data using ABI's Bioscope software.

I have run into an issue that I am not sure how to solve or what the problem is. Essentially, we have to samples from the same subject where the DNA was derived from different tissues, and we are trying to compare. The alignmnets worked well and have nice coverage (~60X). I am having two issues:
1. The SNP calling seems to miss many of the SNPs. When I view the SNPs in the IGV there are clearly SNPs at a location in both of the paried samples, but it was not called in the corresponding sample. I have tried many different settings and am keep getting similiar results.
2. No indels are being called at all, also not sure why?

Does anyone have any thoughts? Would a different set of software be better to use or could the issue be with the inital alignment step?

Thanks all for helping a new commer to the sequencing world!

drio · 01-21-2011, 05:19 AM

1. Take a screenshot of IGV for that region and send it over to ABi. They will tell you what's going on. You can also paste it here.

2. Typically ABi implements indel calling in a different submodule, not in the snpcalling tool. Is it possible you have to enable or run some other piece within Bioscope? Again, ABi should be be able to assist you.

aguffanti · 01-29-2011, 06:12 AM

Hi! I made 12 full exomes and I just recently discovered that diBayes, for whatever reason, tends to call too few aligned reads even where there is noce read coverage. As a consequence, SNPs may be called falesly or missed. I am investigating on this issue. As far as indels are concerned, instead, the software works. You should contact me and let me know which procdedure you used, because there seems to be an undocumnented step in the Bioscope manual: alessandro.guffanti@genomnia.com

HTH

Alessandro

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01-20-2011, 12:12 PM	#1
elondin Junior Member Location: PA Join Date: Jan 2011 Posts: 2	Analyzing data with bioscope Hi all, I am in the midst of doing my first exome sequencing data analyis project. The experiment involved paired-end sequencing and am starting to analyze the data using ABI's Bioscope software. I have run into an issue that I am not sure how to solve or what the problem is. Essentially, we have to samples from the same subject where the DNA was derived from different tissues, and we are trying to compare. The alignmnets worked well and have nice coverage (~60X). I am having two issues: 1. The SNP calling seems to miss many of the SNPs. When I view the SNPs in the IGV there are clearly SNPs at a location in both of the paried samples, but it was not called in the corresponding sample. I have tried many different settings and am keep getting similiar results. 2. No indels are being called at all, also not sure why? Does anyone have any thoughts? Would a different set of software be better to use or could the issue be with the inital alignment step? Thanks all for helping a new commer to the sequencing world!

01-21-2011, 05:19 AM	#2
drio Senior Member Location: 41°17'49"N / 2°4'42"E Join Date: Oct 2008 Posts: 323	1. Take a screenshot of IGV for that region and send it over to ABi. They will tell you what's going on. You can also paste it here. 2. Typically ABi implements indel calling in a different submodule, not in the snpcalling tool. Is it possible you have to enable or run some other piece within Bioscope? Again, ABi should be be able to assist you. __________________ -drd

01-29-2011, 06:12 AM	#3
aguffanti Member Location: Milano, Italy Join Date: Dec 2008 Posts: 29	Me too.. Hi! I made 12 full exomes and I just recently discovered that diBayes, for whatever reason, tends to call too few aligned reads even where there is noce read coverage. As a consequence, SNPs may be called falesly or missed. I am investigating on this issue. As far as indels are concerned, instead, the software works. You should contact me and let me know which procdedure you used, because there seems to be an undocumnented step in the Bioscope manual: alessandro.guffanti@genomnia.com HTH Alessandro