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Part 2 #932 Checking recurrence in combined snv calls #948

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Part 2 #932 Checking recurrence in combined snv calls #948

wants to merge 49 commits into from

Commits on Feb 3, 2021

  1. recurrence strelka

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    kgaonkar6 committed Feb 3, 2021
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  2. n>-2

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    kgaonkar6 committed Feb 3, 2021
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Commits on Feb 4, 2021

  1. add Protein_position

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    kgaonkar6 committed Feb 4, 2021
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Commits on Feb 5, 2021

  1. combined snv

    @kgaonkar6
    kgaonkar6 committed Feb 5, 2021
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Commits on Feb 8, 2021

  1. snv-recurrence

    @kgaonkar6
    kgaonkar6 committed Feb 8, 2021
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  2. re-run filter more than 2

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    kgaonkar6 committed Feb 8, 2021
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  3. removeing old folder

    @kgaonkar6
    kgaonkar6 committed Feb 8, 2021
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  4. removing unused functions

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    kgaonkar6 committed Feb 8, 2021
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  5. add a readme

    @kgaonkar6
    kgaonkar6 committed Feb 8, 2021
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  6. Update README.md

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    kgaonkar6 authored Feb 8, 2021
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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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    kgaonkar6 committed Feb 8, 2021
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  9. combine types

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    kgaonkar6 committed Feb 8, 2021
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  10. uniq

    @kgaonkar6
    kgaonkar6 committed Feb 8, 2021
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  11. Update README.md

    @kgaonkar6
    kgaonkar6 authored Feb 8, 2021
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  12. Update README.md

    @kgaonkar6
    kgaonkar6 authored Feb 8, 2021
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  13. Update README.md

    @kgaonkar6
    kgaonkar6 authored Feb 8, 2021
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  14. comment edits

    @kgaonkar6
    kgaonkar6 committed Feb 8, 2021
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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

    @kgaonkar6
    kgaonkar6 authored Feb 9, 2021
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  2. update brain-goi

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    kgaonkar6 committed Feb 9, 2021
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  3. Merge branch 'recurrence-snv' of https://github.com/kgaonkar6/OpenPBT… 

    …A-analysis into recurrence-snv
    @kgaonkar6
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  4. Merge branch 'master' into recurrence-snv

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    kgaonkar6 authored Feb 9, 2021
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Commits on Feb 10, 2021

  1. Merge branch 'master' into recurrence-snv

    @kgaonkar6
    kgaonkar6 authored Feb 10, 2021
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Commits on Feb 12, 2021

  1. updating cols to use

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    kgaonkar6 committed Feb 12, 2021
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  2. Merge branch 'recurrence-snv' of https://github.com/kgaonkar6/OpenPBT… 

    …A-analysis into recurrence-snv
    @kgaonkar6
    kgaonkar6 committed Feb 12, 2021
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  3. adding plots

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    kgaonkar6 committed Feb 12, 2021
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  4. Merge branch 'master' into recurrence-snv

    @kgaonkar6
    kgaonkar6 authored Feb 12, 2021
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  5. add uniq hits plots

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    kgaonkar6 committed Feb 12, 2021
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  6. Merge branch 'recurrence-snv' of https://github.com/kgaonkar6/OpenPBT… 

    …A-analysis into recurrence-snv
    @kgaonkar6
    kgaonkar6 committed Feb 12, 2021
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Commits on Feb 17, 2021

  1. added dbSNP_RS

    @kgaonkar6
    kgaonkar6 committed Feb 17, 2021
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  2. Merge branch 'master' into recurrence-snv

    @kgaonkar6
    kgaonkar6 authored Feb 17, 2021
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Commits on Feb 18, 2021

  1. adding upset plots for each type of calls

    @kgaonkar6
    kgaonkar6 committed Feb 18, 2021
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  2. pull updates

    @kgaonkar6
    kgaonkar6 committed Feb 18, 2021
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Commits on Feb 19, 2021

  1. update to snv-caller path

    @kgaonkar6
    kgaonkar6 committed Feb 19, 2021
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  2. adding comments for maf creation

    @kgaonkar6
    kgaonkar6 committed Feb 19, 2021
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  3. remove swp files

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    kgaonkar6 committed Feb 19, 2021
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  4. adding upset function

    @kgaonkar6
    kgaonkar6 committed Feb 19, 2021
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  5. independent samples in recurrence

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    kgaonkar6 committed Feb 19, 2021
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Commits on Feb 22, 2021

  1. adding Ref_Allele Tumor_Allele to recurrence

    @kgaonkar6
    kgaonkar6 committed Feb 22, 2021
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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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    kgaonkar6 and jharenza authored Feb 22, 2021
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  3. Update analyses/hotspots-detection/01-reccurence-hotspot-overlap.Rmd 

    Co-authored-by: Jo Lynne Rokita <jharenza@gmail.com>
    @kgaonkar6 @jharenza
    kgaonkar6 and jharenza authored Feb 22, 2021
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  4. Update analyses/hotspots-detection/01-reccurence-hotspot-overlap.Rmd 

    Co-authored-by: Jo Lynne Rokita <jharenza@gmail.com>
    @kgaonkar6 @jharenza
    kgaonkar6 and jharenza authored Feb 22, 2021
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  5. divided scrit to only check and qc recurrence

    @kgaonkar6
    kgaonkar6 committed Feb 22, 2021
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  6. combine and filter

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    kgaonkar6 committed Feb 22, 2021
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  7. re-dp script 1

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    kgaonkar6 committed Feb 22, 2021
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Commits on Feb 23, 2021

  1. pull combine-snv changes

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    kgaonkar6 committed Feb 23, 2021
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  2. re-run

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    kgaonkar6 committed Feb 23, 2021
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Commits on Feb 26, 2021

  1. re-run with collapsed gene anno

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    kgaonkar6 committed Feb 26, 2021
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