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Variant depth cut off - justification

Hello,

I am trying to find some studies or reports that suggest exactly what type of variant depth we should be using as a cut off in WES or general variant calling - I have seen the numbers 5, 10 and 30 flying around but I want to be able to justify my cut off whilst also not cutting off potentially real variants.

Does anyone know of any good papers or studies? I have had a google but can't find anything great. These are not trios.

Thanks! Amy

vcf depth variant
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updated by dthorbur dthorbur • written by hello_bioinf • hello_bioinf

1 answer

I think picking a threshold needs to be made in relation to the data. If you have a target coverage threshold of 100x, then 5x would be a very low threshold, and 30x would be more reasonable.

I would plot your coverage, so you can see how much data you'd be losing and make an informed decision rather than picking an arbitrary value from the literature.

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written by dthorbur dthorbur

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