niu-lab / msisensor2

Microsatellite instability (MSI) detection for tumor only data.
GNU General Public License v3.0
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using .bam file hosted on AWS S3 #23

Closed BastienNguyen closed 2 years ago

BastienNguyen commented 3 years ago

Is there a way to use msisensor2 with .bam stored on AWS S3 opendata? I tried this; msisensor2 msi -M /models_hg19_GRCh37 -t s3://gdc-ccle-2-open/02b56f2a-6813-4afe-88be-50c00ed9db55/test.bam But it doesn't work. Is there a workaround? Thanks!