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Commits on Aug 30, 2024

• singularity alternative as comment

  

  Luis Arge

  committed
  2150c9d

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• input flag fixed

  

  Luis Arge

  committed
  0ac77ec

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• no scaffold version

  

  Luis Arge

  committed
  b0c1142

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• tmp and gatk pathway fixed

  

  Luis Arge

  committed
  4994ac7

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• Input flag fixed

  

  Luis Arge

  committed
  d32a8ff

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• PNG to PDF

  

  Luis Arge

  committed
  bf02b68

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• No alteration...

  

  Luis Arge

  committed
  43f3ced

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• BRAG project with working modules second push

  

  Luis Arge

  committed
  5214179

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Commits on Aug 29, 2024

• BRAG project with working modules

  

  Luis Arge

  committed
  4d8de52

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Commits on Mar 17, 2023

• Update utils.sh

  rakakp007

  authored
  c03c5ce

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Commits on Jan 5, 2023

• allow user to subset vcf by chr to generate percentiles of unfilt vcf, resolves issue of excessive memory req for parts of handler

  ChaochihL

  committed
  f23ec7a

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Commits on Dec 2, 2022

• change /panfs/roc path to /panfs/jay

  ChaochihL

  committed
  c1e6fbb

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Commits on Aug 19, 2022

• fix tmp dir creation error for recalibrating indels only

  ChaochihL

  committed
  98d4d9a

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Commits on Jun 6, 2022

• add zenodo doi link to citation

  ChaochihL

  committed
  871c11f

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Commits on Jun 2, 2022

• add version 3 citation (still need DOI link)

  ChaochihL

  committed
  178f3e4

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• fix graph ann, requires uncompressed VCF

  ChaochihL

  committed
  e2f8a55

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Commits on May 2, 2022

• use better example in comments

  ChaochihL

  committed
  e69074b

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• add script to generate re-run array indices that are formatted

  ChaochihL

  committed
  a7f80f5

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Commits on Mar 17, 2022

• fix error where samples variable doesn't exist

  ChaochihL

  committed
  2536bf0

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Commits on Feb 28, 2022

• change python that gets loaded, was ML python installation was causing issues with samtools accessing a library

  ChaochihL

  committed
  6bd5fdb

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Commits on Feb 15, 2022

• add gzip helper script

  ChaochihL

  committed
  5a1b0fd

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• fix variable name and add annotations to extract

  ChaochihL

  committed
  7c3e9e6

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• fix when cleanup step occurs

  ChaochihL

  committed
  520add1

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• fix tmp dir variable

  ChaochihL

  committed
  d5dc71d

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Commits on Jan 15, 2022

• make tmp dir

  ChaochihL

  committed
  e0672d2

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Commits on Nov 18, 2021

• fix inconsistent out directory variable name

  ChaochihL

  committed
  79bc027

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Commits on Nov 16, 2021

• correct typo on module loading and comment out line, unclear where python-epd is needed

  ChaochihL

  committed
  e4bffc7

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Commits on Aug 10, 2021

• correct usage message file suffix

  ChaochihL

  committed
  15a924a

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• fix typo

  ChaochihL

  committed
  dc1ee32

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Commits on Jul 12, 2021

• make temp directory if tmp variable isn't empty

  ChaochihL

  committed
  7616d69

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Commits on Jun 24, 2021

• fix coverage mapping

  ChaochihL

  committed
  57e1bd3

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Commits on May 28, 2021

• fix missing closing parenthesis in plotting script

  ChaochihL

  committed
  973455a

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Commits on May 18, 2021

• update filtering

  ChaochihL

  committed
  6684149

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Commits on May 3, 2021

• fix stalling during checkDict/createDict function calls when ref dictionary doesn't exist

  ChaochihL

  committed
  2a146a8

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Commits on Apr 28, 2021

• use GATK v3.8.1 for indel realigner, resolves error StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory...

  ChaochihL

  committed
  4fea628

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