search

niu-lab / msisensor2

Microsatellite instability (MSI) detection for tumor only data.
GNU General Public License v3.0
88 stars 21 forks source link

Minimum coverage of WGS? #25

Open byemypast opened 2 years ago

byemypast commented 2 years ago

Dear author, I am going to apply msisensor on my low-coverage WGS data to predict MSI, whereas I found sth wrong may happen with low-coverage data in old Issues. So would you kindly suggest on the minimum coverage WGS that msisensor supported? Thanks

Best regards, Junyi

Beifang commented 2 years ago

We trained the models using TCGA wes data. based on our test cases, coverage >= 30 works very well, but we can not actually access ICGC WGS data for training and test.