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niu-lab / msisensor2

Microsatellite instability (MSI) detection for tumor only data.
GNU General Public License v3.0
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Clarification on -c option #50

Closed KDasu-OneCell closed 3 weeks ago

KDasu-OneCell commented 1 month ago

Hi,

Could you clarify what measure of coverage the -c option for the msi command represents? Is it coverage depth (in reads) or width (in base pairs)?

ZhaoDanOnGitHub commented 1 month ago

您好，您的邮件已收到！

Beifang commented 3 weeks ago

You can understand it as depth, which is actually the total read count covering each ms site. For example, consider the following site:

chr1 25256278 ATCTT 5[GCC] GCAGG N: 0 0 0 16 279 1 0 0 0 0 T: 0 0 2 27 666 0 0 0 0 0

In the normal sample, the depth is calculated as 16+279+1=296, and in the tumor sample, the depth is 2+27+666=695.