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Variant Analysis Of Sanger-Only Sequencing Data

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.

sanger sequencing variant analysis mutation prediction
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updated by Istvan Albert Istvan Albert • written by dra.explota • dra.explota

1 answer

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.

• 24 views • link
written by Istvan Albert Istvan Albert

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

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written by dra.explota • dra.explota

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