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CNV consensus (3 of n): Filter bad segments #328

Merged
merged 26 commits into from
Dec 17, 2019
Merged

CNV consensus (3 of n): Filter bad segments #328

merged 26 commits into from
Dec 17, 2019

Commits on Dec 11, 2019

  1. add step 3 to Snakefile

    Duong committed Dec 11, 2019
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  2. Add file

    Duong committed Dec 11, 2019
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  3. Add files

    Duong committed Dec 11, 2019
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  4. add file

    Duong committed Dec 11, 2019
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  5. add file

    Duong committed Dec 11, 2019
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  6. add file

    Duong committed Dec 11, 2019
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Commits on Dec 12, 2019

  1. Merge branch 'master' into filter_bad_segments

    @fingerfen
    fingerfen authored Dec 12, 2019
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Commits on Dec 13, 2019

  1. Merge branch 'master' into filter_bad_segments

    @fingerfen
    fingerfen authored Dec 13, 2019
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  2. Simplify snakemake 

    Taking advantage of some snakemake features to reduce redundancy.
    @jashapiro
    jashapiro committed Dec 13, 2019
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  3. spelling fix

    @jashapiro
    jashapiro committed Dec 13, 2019
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Commits on Dec 16, 2019

  1. Update analyses/copy_number_consensus_call/Snakefile 

    Co-Authored-By: jashapiro <jashapiro@gmail.com>
    @fingerfen @jashapiro
    fingerfen and jashapiro authored Dec 16, 2019
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  2. Merge branch 'filter_bad_segments' into jashapiro/simplify-snakemake

    @fingerfen
    fingerfen authored Dec 16, 2019
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  3. Merge pull request #1 from jashapiro/jashapiro/simplify-snakemake 

    Simplify snakemake
    @fingerfen
    fingerfen authored Dec 16, 2019
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  4. changed file

    Duong committed Dec 16, 2019
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  5. changed Snakemake

    Duong committed Dec 16, 2019
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  6. Switch to tabs for filter output 

    Also adds filtered `del` files.
    @jashapiro
    jashapiro committed Dec 16, 2019
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  7. Add "chr" to output files that don't have them 

    This makes all files uniform bed format files.
    @jashapiro
    jashapiro committed Dec 16, 2019
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Commits on Dec 17, 2019

  1. add re.split

    Duong committed Dec 17, 2019
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  2. add black_list generating script

    Duong committed Dec 17, 2019
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  3. Update analyses/copy_number_consensus_call/src/scripts/generate_black… 

    …_list.sh

Co-Authored-By: jashapiro <jashapiro@gmail.com>
    @fingerfen @jashapiro
    fingerfen and jashapiro authored Dec 17, 2019
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  4. Merge pull request #2 from jashapiro/jashapiro/entab 

    Switch to tabs for filter output
    @fingerfen
    fingerfen authored Dec 17, 2019
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  5. changed extension to bed

    Duong committed Dec 17, 2019
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  6. Rename bad_chromosomal_seg_updated_merged.txt to bad_chromosomal_seg_… 

    …updated_merged.bed
    @jashapiro
    jashapiro authored Dec 17, 2019
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  7. Comment line

    @jashapiro
    jashapiro authored Dec 17, 2019
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  8. Merge branch 'master' into filter_bad_segments

    @jaclyn-taroni
    jaclyn-taroni authored Dec 17, 2019
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  9. Merge branch 'master' into filter_bad_segments

    @jaclyn-taroni
    jaclyn-taroni authored Dec 17, 2019
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