I want to do DNA mutation analysis by NGS using Ion Torrent PGM sequencing instrument. I will make use of "Ion Ampliseq cancer hotspot panel v2" to amplify cancer mutation hotspots.
May I know how much coverage (X) is sufficient to detect variants (SNPs, indels)?
Dear Mandal,
Higher the coverage of the data, the more reliable the results will be. I did carry out 75X recently.
You are using a targeted panel, so you are going to end up with very deep sequencing of your samples. You probably don't need to worry about minimum coverage, unless you are pooling hundreds of samples and using the lowest throughput chip. It is not unusual to have over 1000X coverage for your targeted regions in a panel.
If you were sequencing exomes, that would be a different story. I agree with Khadim above that you would then be wanting to aim for at least 75x for germline variants, >100X for somatic variants.
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