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bioinform / neusomatic

NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection
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It takes several days to preprocess BAM files for testing #51

Open jingmeng-bioinformatics opened 4 years ago

jingmeng-bioinformatics commented 4 years ago

Hi Sayed, I started preprocessing the whole genome bam files (tumor and matched normal) for testing on my local computer (--number_threads 1) four days ago, and it has not finished now. Why it takes such long time to preprocess the whole genome bam files?

msahraeian commented 4 years ago

@jingmeng-bioinformatics It depends on your sample coverages. For me, I usually run on a 28-threads cluster and it will take a couple of hours. So, If you run on 1 thread it may take a few days.

jingmeng-bioinformatics commented 4 years ago

Ok, thank you for your reply.