Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Warn or raise an exception when CollectDuplexSeqMetrics is run on a consensus BAM #992

Closed
clintval opened this issue May 28, 2024 · 0 comments · Fixed by #1003
Closed

Warn or raise an exception when CollectDuplexSeqMetrics is run on a consensus BAM #992

clintval opened this issue May 28, 2024 · 0 comments · Fixed by #1003

Comments

@clintval
Copy link
Member

It is possible to run the tool CollectDuplexSeqmetrics on a consensus BAM file but the results will not be intuitively correct since metrics collection is expecting the input be raw reads (and not consensus sequences) annotated with the MI tag:

|1. The exact BAM output by the `GroupReadsByUmi` tool (in the sort-order it was produced in)
|2. A BAM file that has MI tags present on all reads (usually set by `GroupReadsByUmi` and has
| been sorted with `SortBam` into `TemplateCoordinate` order.

We should either support gathering metrics over the consensus BAM or raise an exception for unsupported behavior if any of the consensus SAM tags are encountered.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging a pull request may close this issue.

1 participant