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V6 release #190

Merged
merged 3 commits into from
Oct 30, 2019
Merged

V6 release #190

merged 3 commits into from
Oct 30, 2019

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yuankunzhu
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Purpose/implementation

data release updates for v6

  • changes:
    • Clinical file updates:
      • Missing aliquot_id and sample_id added
      • Updated broad_composition to cell line for WGS samples denoted as Cell line
      • Removed duplicate BS_4M0ZMCDC with wrong age at diagnosis
      • Add cohort column for CBTTC or PNOC003 samples
      • Tumor specimens missing composition were changed to Solid Tumor
      • Blood specimens missing primary_site were changed to Peripheral Whole Blood
      • Updated age_at_diagnosis to earliest age reported (same age used in OS calculations)
      • Updated OS_days and OS_status based on updated clinical data
      • Added cancer_predispositions information
      • Added seq_center (could not add seq_instrument at this time due to multiple entries for BS_IDs)
      • Harmonized Diagnosis and Initial CNS Tumor for tumor_descriptor field
      • Changed Relapse sample to Progressive (DIPG sample truly progressive, not relapse)
      • Add tumor purity derived from Theta2 (normal_fraction and tumor_fraction)
      • Add glioma_brain_region for low- and high-grade gliomas
        ​
    • SV:
      • Removed LUMPY data, as additional benchmarking to remove normal SVs needs to be done. We may not include this in a future release.
        ​
    • SNV:
      • Re-ran BS_7KR13R3P using targeted panel bed files; removed WXS calls from MAFs
      • Added WXS calls to all MAFs
      • Added targeted panel bed and padded bed files
        ​
    • CNV:
      • Re-ran ControlFreeC and CNVkit with optional BAF inputs; Added Theta2 purity correction to CNVkit
      • Added copy number to CNVkit and removed ControlFreeC seg file

Issue/Caveats

Directions for reviewers

changed on release notes and download script.

  • file content updated for
    • pbta-cnv-cnvkit.seg.gz
    • pbta-histologies.tsv
    • pbta-snv-lancet.vep.maf.gz
    • pbta-snv-mutect2.vep.maf.gz
    • pbta-snv-strelka2.vep.maf.gz
    • pbta-snv-vardict.vep.maf.gz
    • pbta-sv-manta.tsv.gz
  • add file
    • StrexomeLite_Targets_CrossMap_hg38_filtered_chr_prefixed.bed
    • StrexomeLite_hg38_liftover_100bp_padded.bed
  • remove file
    • pbta-sv-lumpy.tsv.gz
    • pbta-cnv-controlfreec.seg.gz

Results

Docker and continuous integration

@yuankunzhu yuankunzhu changed the title Release/v6 V6 release Oct 30, 2019
jaclyn-taroni
jaclyn-taroni approved these changes Oct 30, 2019
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Looks good to me! Thank you!

@jaclyn-taroni jaclyn-taroni merged commit 55690dc into AlexsLemonade:master Oct 30, 2019
@jaclyn-taroni jaclyn-taroni mentioned this pull request Oct 30, 2019
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4 tasks
jaclyn-taroni added a commit to cansavvy/OpenPBTA-analysis that referenced this pull request Oct 30, 2019
@jaclyn-taroni
Make sure AlexsLemonade#190 changes are included
acab221 
I'm not sure what went wrong
jaclyn-taroni pushed a commit that referenced this pull request Oct 30, 2019
@cansavvy @jaclyn-taroni
PR 2 of 4 for SNV Consensus: Merge callers script (#184)
4e033ba 
* Set up the set up

* Add circle CI test and Docker config

* Add some more comments

* Set up Rprojroot for circle CI test to work better

* Fixing Circle CI file.

* Change read_tsv to data.table::fread for big file

* read in the .gz file

* push plot function changes

* Fix an error

* Add missing package to Dockerfile

* Reduce cosmic file to only the brain sample mutations

* Update README with changes to cosmic file

* re-updated Dockerfile

* Ran a linter on set up script

* Comment out of date

* Get rid of old WGX/WXS bed file set up

* Incorporate initial PR suggestions from @jashapiro and @cbethell

* Push a working bash script

* Add bash script to circle CI

* Add usage section in README and change name of script

* Add some more comments

* Correct a couple things in the README

* Get rid of remnant comment

* Fix a typo!

* Add Usage to the TOC

* Add more documentation to the README

* Update Circle CI

* Push more exact bash script

* Fix a couple issues with handling metadata file path

* Get rid of dev remnants

* Couple changes for readability

* Add some things to README and get rid of part of bash that isn't there

* Found dumb mistake

* Changed [*] to [+]

* I mean [*] to a [@] which makes more sense.

* Fix some of the overwrite handling

* Add template and report script

* Add run_eval to bash script

* Get rid of dev remnants

* Make better handling of strategy that is called but not there

* Get rid of dev remnant again

* Get rid of stray `\`

* File got misplaced

* Get rid of cosmic mutations without proper coordinates

* Fixed a wrinkle with the COSMIC file

* re-run a linter on everything.

* Couple more minor touches

* Make set up files not run if they are already existing

* Fix handling of COSMIC file creation

* Incorporate @jashapiro 's suggestions

* Add a few more @jashapiro suggestions

* Circle CI does not have a kitematic directory. Get rid

* Make warning instead of stop

* Missing `ggplot2::`

* Remove reference files after use to try to reduce memory usage

* Make one big mutate

* Dumb extra comma

* Add VAF_FILTER option and it's circle CI component

* get rid of typo

* Re-fix Circle CI file

* Fix WXS if statement

* Fix default Circle CI option

* Make indels come last in the barplot

* Fix order of barplot graph

* Add the comparison notebook

* Add initial comparison notebook

* Notebook adjustments

* Fixed dumb label mix-up problem

* Further honing things

* Added the other plots except that one combo plot

* Add rendered version too

* Rough draft of all plots here

* Get rid of upsettR's blank plot

* Refresh the notebook

* Run linter

* Change name to reflect the data better

* Add to CircleCI and Dockerfile

* Try to fix busted CircleCI command

* Attempt to fix Dockerfile build problem

* Attempt to fix docker build

* Some Docker probs fixed

* Push latest notebook and Dockerfile

* Dockerfile appears to be building right.

* Couple more things to finish up Dockerfile adds

* development thing was left

* Add Template for results discussion

* Updates to notebook. Function and etc.

* Refresh notebook

* Add png saves to each plot

* Added options to calculate_vaf_tmb.R script

* Add set up for vaf_filter experiment

* Push separate notebook for vaf_filter exp

* Changes to README

* Add more documentation

* Push VAF cutoff experiment notebook

* Update title of vaf notebook

* Update notebook

* Fix path problem and also extend no_region option

* Fix typo

* Added some documentation

* Prep consensus mutation file saving

* Fix sex chr mislabeling in COSMIC file per @jashapiro 's suggestion

* Get rid of regional analysis. Linter the notebooks Add changes to plots

* Updated COSMIC file

* Streamline this branch

* Revert unneeded changes

* Clean up README

* Add --no_region option to README

* Update CircleCI

* Get rid of region analysis to save on memory usage

* Add documentation about comparison to README

* Linter and switch to rds

* Upload results

* refresh notebook and results

* Updated notebook

* Change name of bash script and make it run the notebook too

* Update README

* column problem *should* be fixed

* Push refreshed notebook and results

* Add a bit more info in the README

* attempt to fix CircleCI's lack of grid package

* Add grid to Dockerfile explicitly

* Made some things a tad less janky

* Push refreshed notebook. Get rid of grid install from Dockerfile

* Try older version of UpSetR for shiggles

* Get rid of `library(grid)` so we know if the version of UpSetR has it fixed

* Test CRAN installation fo UpSetR

* beginning to reformulate script organization for consensus file creation

* Push reorganized scripts and notebooks

* renaming and reorganzing and styling

* suppressWarnings for coercing variables. We expect that

* get rid of some development remnants

* Streamline the PR

* Get rid of dummy file

* Streamline even more

* Get rid of superfluous pound signs

* Actually add merge callers script

* get rid of outdated source(functions)  command

* Make --overwrite actually functional

* re-run linter after those adds

* Get rid of outdated `-w`

* Fix example

* Found an outdated comment

* Address the outdated comments spotted by @jaclyn-taroni

* Make sure #190 changes are included

I'm not sure what went wrong
@jaclyn-taroni jaclyn-taroni mentioned this pull request Oct 31, 2019
Closed
@cansavvy cansavvy mentioned this pull request Oct 31, 2019
Merged
@yuankunzhu yuankunzhu deleted the release/v6 branch November 1, 2019 00:07
@jharenza jharenza mentioned this pull request Nov 1, 2019
Closed
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@yuankunzhu @jaclyn-taroni