Variant Analysis Of Sanger-Only Sequencing Data

Question

[dra.explota]

Hi Everyone!

I am working with Sanger Sequencing (no NGS), I had previously only used Sanger to validate primers or my NGS data. Now I am sequencing a relatively small region of high homology to others using Sanger. I am wondering what is the most efficient work-flow to analyze variants.

I know I can just make my data fit one of the formats required by Annovar or SeattleSeq and get some output, but I am unsure on whether this is the correct approach, I also wonder if there is anything else out there specifically for Sanger or that has the actual consideration of a Sanger "input".

Thanks in advance, Dra. E.

Answer 1

[Istvan Albert]

The high throughput tools are used to reduce the data to a smaller manageable size. They are almost always characterized by non-trivial rates of error but we still use them as any other approach would be unfeasible.

Once that is done and there are only a few locations manual inspection and analysis of each of the sites is the best way to get the most out of the data.

I would recommend to use Annovar or other tools to get started with annotating the variants, but after that laying the data over other known information sources is the best approach.

[dra.explota]

Thanks! (I was away from the office, sorry for the late acknowledgement!)