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

2 stars 6 forks source link

Automatic flags based on size of BAM file #6

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 inputs.

samanvp commented 5 years ago

It seems since I forked my repo when the original repo was private, this PR doesn't get updated when I pushed new commits to the forked branch. I prepared a new PR that has all the changes you asked for. After your confirmation, I will close this PR.

Sorry for inconvenience...

kemp-google commented 5 years ago

Thanks, sorry again for the trouble with the repository - yay for being public now :)