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#819 Part2 : Scavenge back hotspots to add to consensus calls #961

Merged
merged 144 commits into from
May 13, 2021
Merged

#819 Part2 : Scavenge back hotspots to add to consensus calls #961

merged 144 commits into from
May 13, 2021

Commits on Feb 3, 2021

  1. recurrence strelka

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  2. n>-2

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Commits on Feb 4, 2021

  1. add Protein_position

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Commits on Feb 5, 2021

  1. combined snv

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Commits on Feb 8, 2021

  1. snv-recurrence

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  2. re-run filter more than 2

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  3. removeing old folder

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  4. removing unused functions

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  5. add a readme

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  6. Update README.md

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  7. combine types

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  8. Merge branch 'recurrence-snv' of https://github.com/kgaonkar6/OpenPBT… 

    …A-analysis into recurrence-snv
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  9. combine types

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  10. uniq

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  11. Update README.md

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  12. Update README.md

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  13. Update README.md

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  14. comment edits

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  15. Merge branch 'recurrence-snv' of https://github.com/kgaonkar6/OpenPBT… 

    …A-analysis into recurrence-snv
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Commits on Feb 9, 2021

  1. Merge branch 'master' into recurrence-snv

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  2. update brain-goi

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  3. Merge branch 'recurrence-snv' of https://github.com/kgaonkar6/OpenPBT… 

    …A-analysis into recurrence-snv
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  4. Merge branch 'master' into recurrence-snv

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Commits on Feb 10, 2021

  1. Merge branch 'master' into recurrence-snv

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Commits on Feb 12, 2021

  1. updating cols to use

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  2. Merge branch 'recurrence-snv' of https://github.com/kgaonkar6/OpenPBT… 

    …A-analysis into recurrence-snv
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  3. adding plots

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  4. Merge branch 'master' into recurrence-snv

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  5. add uniq hits plots

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  6. Merge branch 'recurrence-snv' of https://github.com/kgaonkar6/OpenPBT… 

    …A-analysis into recurrence-snv
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Commits on Feb 17, 2021

  1. added dbSNP_RS

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  2. Merge branch 'master' into recurrence-snv

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Commits on Feb 18, 2021

  1. adding upset plots for each type of calls

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  2. pull updates

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Commits on Feb 19, 2021

  1. update to snv-caller path

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  2. adding comments for maf creation

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  3. remove swp files

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  4. adding upset function

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  5. independent samples in recurrence

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Commits on Feb 22, 2021

  1. adding Ref_Allele Tumor_Allele to recurrence

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  2. Update analyses/hotspots-detection/01-reccurence-hotspot-overlap.Rmd 

    Co-authored-by: Jo Lynne Rokita <jharenza@gmail.com>
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  3. Update analyses/hotspots-detection/01-reccurence-hotspot-overlap.Rmd 

    Co-authored-by: Jo Lynne Rokita <jharenza@gmail.com>
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  4. Update analyses/hotspots-detection/01-reccurence-hotspot-overlap.Rmd 

    Co-authored-by: Jo Lynne Rokita <jharenza@gmail.com>
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  5. combine and filter

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  6. re-dp script 1

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Commits on Mar 2, 2021

  1. filter for known hotspots only

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  2. Merge branch 'master' into combine-snv

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  3. Delete brain-goi-list-new.txt

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  4. add html

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  5. Merge branch 'combine-snv' of https://github.com/kgaonkar6/OpenPBTA-a… 

    …nalysis into combine-snv
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Commits on Mar 4, 2021

  1. add images

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  2. add comments

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Commits on Mar 11, 2021

  1. adding all maf columns in filtered file

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  2. run script

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  3. add per caller filters

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  4. add per caller filters

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Commits on Mar 12, 2021

  1. Delete 01-combine-maf.Rmd

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  2. Delete 01-combine-maf.nb.html

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  3. Delete combined_maf_hotspots.RDS

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  4. adding vardict subset

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  5. Merge branch 'separated_callers_filter' of https://github.com/kgaonka… 

    …r6/OpenPBTA-analysis into separated_callers_filter
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Commits on Mar 15, 2021

  1. files un-committed

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Commits on Mar 16, 2021

  1. Update analyses/hotspots-detection/README.md 

    Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
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  2. Update analyses/hotspots-detection/README.md 

    Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
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  3. Update analyses/hotspots-detection/utils/prepMaf.R 

    Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
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  4. Update analyses/hotspots-detection/utils/prepMaf.R 

    Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
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  5. Update analyses/hotspots-detection/utils/prepMaf.R 

    Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
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  6. Update analyses/hotspots-detection/utils/prepMaf.R 

    Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
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  7. Update analyses/hotspots-detection/run_overlaps_hotspot.sh 

    Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
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  8. Update analyses/hotspots-detection/run_overlaps_hotspot.sh 

    Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
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  9. Update analyses/hotspots-detection/run_overlaps_hotspot.sh 

    Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
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  10. Update analyses/hotspots-detection/00-subset-maf.R 

    Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
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  11. updates

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  12. conflict res

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  13. add just strelka

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Commits on Mar 18, 2021

  1. update grep genes before R filtering

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  2. styling

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  3. removing genes as input param

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  4. subsetByOverlap

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  5. read_tsv seems to assign the columns accurately compared to fread

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  6. add to ci

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  7. add task name

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  8. init

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  9. filter hotspots

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  10. init

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  11. only adding new calls

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  12. adding script to steps

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  13. Update README.md

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Commits on Mar 19, 2021

  1. updating the commits

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Commits on Mar 22, 2021

  1. splice and indel

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  2. Merge branch 'separated_callers_filter' of https://github.com/kgaonka… 

    …r6/OpenPBTA-analysis into combine_hotspots_consensu
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  3. rerun after splice indel addition

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Commits on Mar 23, 2021

  1. adding indels with ? and filter for canonical transcripts

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Commits on Mar 24, 2021

  1. fixing fail because updated file was not committed

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Commits on Mar 26, 2021

  1. Update analyses/hotspots-detection/utils/filterMaf.R 

    Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
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  2. Update analyses/hotspots-detection/utils/filterMaf.R 

    Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
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  3. Update analyses/hotspots-detection/run_overlaps_hotspot.sh 

    Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
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  4. Update analyses/hotspots-detection/utils/filterMaf.R 

    Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
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  5. Update analyses/hotspots-detection/00-subset-maf.R 

    Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
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    kgaonkar6 and jashapiro authored Mar 26, 2021
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  6. description update

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  7. description update conflict res

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    kgaonkar6 committed Mar 26, 2021
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  8. asuggested changes from review;comments update

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Commits on Mar 29, 2021

  1. add error if MSKCC hotspot is not complete

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  2. uniq gene list

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Commits on Apr 5, 2021

  1. Merge branch 'master' into combine_hotspots_consensu

    @kgaonkar6
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Commits on Apr 12, 2021

  1. Update analyses/hotspots-detection/01-create-hotspot-maf.Rmd 

    Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>
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    kgaonkar6 and jashapiro authored Apr 12, 2021
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Commits on Apr 13, 2021

  1. Merge branch 'separated_callers_filter' into combine_hotspots_consensu

    @kgaonkar6
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  2. added split_mnv maf_coltypes and variant_type distribution

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Commits on Apr 14, 2021

  1. adding ordered caller info and counts value

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  2. reorg to add vaf filter opt and add caller count info

    @kgaonkar6
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  3. save changes

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  4. rm intermediate files

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  5. adding knit html

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Commits on Apr 21, 2021

  1. conflict resolution

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Commits on Apr 22, 2021

  1. remove vardict only

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  2. gzip

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  3. adding updated html

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Commits on Apr 23, 2021

  1. Merge branch 'master' into combine_hotspots_consensu

    Jo Lynne Rokita authored Apr 23, 2021
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  2. add only hotspots to scavenge back

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  3. removing unintended path dx file commits

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  4. Merge branch 'combine_hotspots_consensu' of https://github.com/kgaonk… 

    …ar6/OpenPBTA-analysis into combine_hotspots_consensu
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Commits on May 4, 2021

  1. update col types

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Commits on May 5, 2021

  1. script to add col types

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  2. adding col types

    @kgaonkar6
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  3. Merge branch 'update-format-snv' into combine_hotspots_consensu

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  4. adding hotspots from latest mafs

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  5. save RMD re-run

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  6. save RMD re-run

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  7. Merge branch 'master' into combine_hotspots_consensu

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Commits on May 11, 2021

  1. remove old RDS

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  2. Merge branch 'combine_hotspots_consensu' of https://github.com/kgaonk… 

    …ar6/OpenPBTA-analysis into combine_hotspots_consensu
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  3. Merge branch 'master' into combine_hotspots_consensu

    @kgaonkar6
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  4. updating oncoprint with AlexsLemonade#1009

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  5. Revert "updating oncoprint with AlexsLemonade#1009" 

    This reverts commit ea4f636.
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Commits on May 12, 2021

  1. saving all hotspots

    Ubuntu committed May 12, 2021
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  2. saving html

    Ubuntu committed May 12, 2021
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  3. update caller collapsed by ;

    Ubuntu committed May 12, 2021
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  4. rerun with unique(filterMaf.R output files)

    Ubuntu committed May 12, 2021
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  5. remove gzfile()

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    kgaonkar6 committed May 12, 2021
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  6. caller collapse with ;

    @kgaonkar6
    kgaonkar6 committed May 12, 2021
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  7. Update README.md

    @kgaonkar6
    kgaonkar6 authored May 12, 2021
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  8. final rerun

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  9. print unique to 1 caller calls in nb

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Commits on May 13, 2021

  1. Merge branch 'master' into combine_hotspots_consensu

    Jo Lynne Rokita authored May 13, 2021
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