varlociraptor / varlociraptor.github.io Goto Github PK

See [Filtering]({{< ref "filtering.md" >}}) below:

See link: https://varlociraptor.github.io/docs/calling/

The live website has a part about tmb estimation with an incomplete command example:

https://varlociraptor.github.io/docs/estimating/

Currently, the command reads:

varlociraptor --coding-genome-size 3e7 --tumor-sample tumor --somatic-tumor-events SOMATIC_TUMOR < calls.annotated.bcf > tmb.vl.json

But it should be (with the correct subcommand estimate tmb included:

varlociraptor estimate tmb --coding-genome-size 3e7 --tumor-sample tumor --somatic-tumor-events SOMATIC_TUMOR < calls.annotated.bcf > tmb.vl.json

As this version of the repo does not contain the respective estimating.md file (see issue #1 ), providing a PR would mess up your history...?

@johanneskoester are some changes you made in a local checkout missing in this main repo? And is this the one, from which the homepage is generated? Because I can't find estimating.md in:

https://github.com/varlociraptor/varlociraptor-homepage/tree/84d4e7b2fa239123258a4bb7bc9c5917a27e5ecc/content/docs