We updated the consensus seg file creation in #1066 to use freec CN calls as default and neutral calls as NA. In this PR we will re-run focal-cn-file-preparation to update the focal cnv files used in other modules.
What was your approach?
Just run run-prepare-cn.sh
What GitHub issue does your pull request address?
related to #964
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
NA
Is there anything that you want to discuss further?
NA
Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?
yes
Results
What types of results are included (e.g., table, figure)?
tables
What is your summary of the results?
Please see discussion in #1010 comparing consensus_seg_annotated_cn_autosomes_freec.tsv.gz and consensus_seg_annotated_cn_x_and_y_freec.tsv.gz from freec+neutral calls as NA, with cnvkit + neutral calls as NA and pervious v18 version (cnvkit +neutral calls as 2)
Reproducibility Checklist
[x] The dependencies required to run the code in this pull request have been added to the project Dockerfile.
[x] This analysis has been added to continuous integration.
Documentation Checklist
[x] This analysis module has a README and it is up to date.
[x] This analysis is recorded in the table in analyses/README.md and the entry is up to date.
[x] The analytical code is documented and contains comments.
⚠️ merge #1066 before this PR
We updated the consensus seg file creation in #1066 to use freec CN calls as default and neutral calls as NA. In this PR we will re-run
focal-cn-file-preparationto update the focal cnv files used in other modules.What was your approach?
Just run run-prepare-cn.sh
What GitHub issue does your pull request address?
related to #964
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
NA
Is there anything that you want to discuss further?
NA
Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?
yes
Results
What types of results are included (e.g., table, figure)?
tables
What is your summary of the results?
Please see discussion in #1010 comparing consensus_seg_annotated_cn_autosomes_freec.tsv.gz and consensus_seg_annotated_cn_x_and_y_freec.tsv.gz from freec+neutral calls as NA, with cnvkit + neutral calls as NA and pervious v18 version (cnvkit +neutral calls as 2)
Reproducibility Checklist
Documentation Checklist
READMEand it is up to date.analyses/README.mdand the entry is up to date.