Automatic flags based on size of BAM file

googlegenomics / gcp-deepvariant-runner

This repository contains a docker container that runs DeepVariant on the Google Cloud Platform.

Apache License 2.0

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Automatic flags based on size of BAM file #5

Closed samanvp closed 5 years ago

samanvp commented 5 years ago

In order to make execution of DeepVariant easier for new users, we introduced an automatic method for setting computational flags based on the size of input BAM file.

This is our best effort to reduce the cost of running DeepVariant. We ran extensive profiling experiments to find the optimal settings for both WGS and WES input files.

samanvp commented 5 years ago

Since this repo was branched a while ago two CLs were missed, specifically:

Decouple gcsfuse initialization from make_examples
Make our unit_tests stronger

Now they are merged with this PR, which is already big, and makes it a bit too complicated. Please let me know if you prefer to make these 3 changes 3 separate PRs or 3 commits.