This repository was archived by the owner on Jun 21, 2023. It is now read-only.
Add context for Vardict number of calls and more on sample seq prep #345
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
jharenza
reviewed
Aug 31, 2022
content/06.methods.md
Outdated
| @@ -125,7 +126,7 @@ This workflow is available in the [D3b GitHub repository](https://github.com/d3b | |||
| ##### SNV and indel calling | |||
|
|
|||
| For PBTA samples, we used four variant callers to call SNVs and indels from panel, WXS, and WGS data: `Strelka2` [@doi:10.1038/s41592-018-0051-x], `Mutect2` [@biorxiv:10.1101/861054], `Lancet` [@doi:10.1038/s42003-018-0023-9], and `VarDictJava` [@doi:10.1093/nar/gkw227]. | |||
| `VarDictJava`-only calls were not retained since ~ 39M calls with low VAF were uniquely called and may be potential false positives. | |||
| `VarDictJava`-only calls were not retained since ~ 39M calls with low VAF were uniquely called and may be potential false positives (~1.2M calls were included in consensus SNV calling described below). | |||
There was a problem hiding this comment.
Was this number in a notebook you can point me to?
There was a problem hiding this comment.
If you read in the consensus MAF, this is the number of rows. It is also what is stated in the module README.
jharenza
reviewed
Aug 31, 2022
|
AppVeyor build 1.0.1048 for commit af96ea1 is now complete. Found 0 potential spelling error(s). Preview:... |
jharenza
approved these changes
Aug 31, 2022
|
AppVeyor build 1.0.1053 for commit 645eac2 is now complete. Found 0 potential spelling error(s). Preview:... |
github-actions bot
pushed a commit
that referenced
this pull request
Aug 31, 2022
[ci skip] This build is based on 6099cc0. This commit was created by the following CI build and job: https://github.com/AlexsLemonade/OpenPBTA-manuscript/commit/6099cc0ebb05c033058a2d2eabbf43bbcc285437/checks https://github.com/AlexsLemonade/OpenPBTA-manuscript/actions/runs/2967307497
github-actions bot
pushed a commit
that referenced
this pull request
Aug 31, 2022
[ci skip] This build is based on 6099cc0. This commit was created by the following CI build and job: https://github.com/AlexsLemonade/OpenPBTA-manuscript/commit/6099cc0ebb05c033058a2d2eabbf43bbcc285437/checks https://github.com/AlexsLemonade/OpenPBTA-manuscript/actions/runs/2967307497
Sign up for free
to subscribe to this conversation on GitHub.
Already have an account?
Sign in.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Here I'm adding the following to the methods section: