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Program to validate NGS variants from Sanger sequencing
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14 months ago
user31888 • 60
United States

Is there a program for checking that a variant detected with NGS is present in Sanger resequencing data (.ab1 file). I tried Thermo Fisher NGS App, but it did not work for me (setup takes ages and file format does not fit apparently).

If such a program does not exist, how do you do to find your variant in the .ab1 file using something like 4Peaks for example?

Thanks !

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The last time that I worked in a clinical genetics laboratory, back in 2014, Sanger data was being manually checked by numerous individuals. The results that I generated from my clinical-grade next generation DNA-sequencing analysis pipeline were also being compared to Sanger manually.

Is there any specific reason why you are looking for an automated way of doing this? Sanger being Sanger, it cannot produce data as rapidly as NGS, so, you must not have that much variants to compare (?).

You may find this old thread of much relevance: Reading Ab1 Files With Python

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Thanks Kevin. I have almost a hundred traces to check manually. I was just wondering if it would exist some kind of automated way.

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I will check with my colleagues in the clinical genetics scene and get back to you.

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Hello, I checked with my colleagues and they use Staden gap4, but I don't believe that it is automated.

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