Question: Program to validate NGS variants from Sanger sequencing
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gravatar for user31888
2.1 years ago by
user3188870
United States
user3188870 wrote:

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 !

validation ngs sanger • 862 views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by user3188870

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

ADD REPLYlink written 2.1 years ago by Kevin Blighe49k

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

ADD REPLYlink written 2.0 years ago by user3188870

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

ADD REPLYlink written 2.0 years ago by Kevin Blighe49k

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

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by Kevin Blighe49k
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