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!
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!
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