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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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tumor only model , number of sites with enough coverage: 0 #24

Open wyy1234-github opened 2 years ago

wyy1234-github commented 2 years ago

Hi, Thank you for developing msisensor2, it's really helpful. I am using this tool in tumor-only model in a 160 gene panel, but the number of sites with enough coverage is 0 (Number of total sites: 18), the coverage seems high enough. chr2 47635523 TGTAC 13[T] AAGGA T: 0 0 0 0 0 0 0 0 2 6 45 383 2619 632 93 7 2 chr2 48032740 TGTGA 13[T] AAGGT T: 0 0 0 0 0 0 0 0 1 18 79 520 2148 334 43 3 4

following is the command: msisensor2 msi -M models_hg19_GRCh37 -t MQP.rmdup.bam -e 160.bed -b 10 -o JMQP.msi

I look forward to your reply.

wyy1234-github commented 2 years ago

we find that the model dir must be 777 permission, meybe it is a bug for the software.