Threshold for variant detection by Haloplex
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6.5 years ago
jonessara770 ▴ 240

Hi guys,

I am newbie in Haloplex data analysis. I have haloplex data from few tumor and normal samples. I mapped them by BWA and did not remove duplicates reads as suggested by the company. I called variants with mpileup.

Now I am wondering what threshold I should put in terms of variant read depths and allele frequencies to say that the detected variants is true and not an artifact? I know my question is very general but any input is highly appreciated.

Also, What statistics do you give for haloplex data?

Thanks Sara

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