While calculating coverage information from WES data one can find some regions covered with very less read depth (say 1,2 or 3). My question is what is the minimum cut-off one should consider to confirm its coverage .
Thanks in advance.
Navonil De Sarkar
We use dynamic hard filter. We consider those regions suitable for variant call where read depth is greater than least 20%.
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Mohamed Ashick
It depends on different factors. For an eg, I wud say even one is enough if that one is uniquely aligned paired end with high base quality and mapping quality; even 5 reads in repeat region with improper pairing and low qualities is ambigous . So I would suggest to use mapping quality and read depth together.
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