{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/4298","repository_url":"https://api.github.com/repos/broadinstitute/gatk","labels_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4298/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4298/comments","events_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4298/events","html_url":"https://github.com/broadinstitute/gatk/issues/4298","id":292568552,"number":4298,"title":"profile different values of DEFAULT_READSHARD_SIZE for 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currently not clear what the best setting for DEFAULT_READSHARD_SIZE is, or how important it is to performance / results.  We should find out."},"comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/issues/comments/363201201","html_url":"https://github.com/broadinstitute/gatk/issues/4298#issuecomment-363201201","issue_url":"https://api.github.com/repos/broadinstitute/gatk/issues/4298","id":363201201,"user":{"login":"droazen","id":798637,"avatar_url":"https://avatars0.githubusercontent.com/u/798637?v=4","gravatar_id":"","url":"https://api.github.com/users/droazen","html_url":"https://github.com/droazen","followers_url":"https://api.github.com/users/droazen/followers","following_url":"https://api.github.com/users/droazen/following{/other_user}","gists_url":"https://api.github.com/users/droazen/gists{/gist_id}","starred_url":"https://api.github.com/users/droazen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/droazen/subscriptions","organizations_url":"https://api.github.com/users/droazen/orgs","repos_url":"https://api.github.com/users/droazen/repos","events_url":"https://api.github.com/users/droazen/events{/privacy}","received_events_url":"https://api.github.com/users/droazen/received_events","type":"User","site_admin":false},"created_at":"2018-02-05T19:51:55Z","updated_at":"2018-02-05T19:51:55Z","author_association":"COLLABORATOR","body":"@tomwhite I think the current value for `DEFAULT_READSHARD_SIZE` might be inappropriate, especially given that `HaplotypeCallerSpark` (unlike the walker version, which is lazy) currently materializes all assembly regions within a shard at once (see https://github.com/broadinstitute/gatk/issues/4301). We should profile with both smaller and larger values for `DEFAULT_READSHARD_SIZE` and see what effect it has."}}
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