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How do I know that a polymorphisms is real?

I have read in some papers; such as : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5282756/

It stablishes that a SNP is real when it has a depth >=10, mapping quality >=20 and SNP quality > =15

Or this: https://www.tandfonline.com/doi/full/10.1080/13102818.2019.1579671

It stabilish that the average coverage =500, central base quality >=20 and SNP frequency >=35%.

It quite confused, because each article establishes a different criteria

Is there any consensus idea about these parameters?

Where can I see the average coverage and central base quality? Thanks in advantage

snp
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written by apl00028 apl00028

Is there any consensus idea about these parameters?

Simple answer: No. That is pretty much the problem for almost any aspect in bioinformatics: Lots of different approaches, some more meaningful than others, but no gold standards. To really have confidence, you would need to validate the variants you call with your pipeline and the respective settings using independent experiments such as Sanger sequencing in the sample you did NGS with.

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written by ATpoint ATpoint

In general, one would sequence the region using appropriate primers to confirm that a polymorphism you are observing is real.

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written by GenoMax GenoMax

agree, lab validation with Sanger or PCR is the final validation

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written by JC JC

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