MANTIS on WGS samples about mantis HOT 5 CLOSED

Hello, and thank you for your interest in MANTIS. We have not tested it on WGS data, however it should function provided sufficient coverage. Could you post median coverage and quality statistics? This would assist in choosing thresholds.

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Hi @rbonneville,

we do have a similar question. We have some tumor/normal paired WGS data with median coverages of ~70-80x. Which other quality statistics do you need or is this sufficient to recommend parameters for MANTIS?

Thanks,
Clemens

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Hi @messersc, do you have any quality statistics, for instance %Q30?

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Hi @rbonneville, the runs look very good in general, the %Q30 is > 95 % for all libraries (this is paired-end, 151 bp data).

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Given the high %Q30 and your median coverages, I would recommend first trying whole exome parameters.

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