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Commits on Jan 5, 2021

• Merge pull request #52 from EDitt/temp

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  ChaochihL

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  a1dfc9c

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Commits on Dec 30, 2020

• Situation for cases of haploid genotype calls

  

  Emily Loring Dittmar

  committed
  747cf7e

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• Situation for cases of haploid genotype calls

  

  Emily Loring Dittmar

  committed
  49a6d77

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Commits on Dec 23, 2020

• make new changes compatible with slurm

  ChaochihL

  committed
  8ec139f

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• Merge pull request #51 from EDitt/Filter_patch

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  ChaochihL

  authored
  71d2e72

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• Merge pull request #50 from EDitt/AnnotationFigs

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  ChaochihL

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  9a2f35b

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• changed variable in output echo statement

  EDitt

  authored
  c541e3a

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• fix handling of tmp dir

  ChaochihL

  committed
  6102321

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Commits on Dec 22, 2020

• add check for properly specified resource file variables

  ChaochihL

  committed
  1940d81

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• add check to reduce run time upon resubmission of job

  ChaochihL

  committed
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Commits on Dec 18, 2020

• fix tmp directory call and add slurm support for Variant_analysis handler

  ChaochihL

  committed
  f0cb18b

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• Add bedtools dependency, remove annotations graphing from GATK3

  EDitt

  committed
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Commits on Dec 17, 2020

• fix missing tmp dir variable call in Variant_Recalibrator handler

  ChaochihL

  committed
  e03774e

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• add slurm support for Variant_Analysis handler

  ChaochihL

  committed
  0173eed

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• add support for .vcf.gz files

  ChaochihL

  committed
  77c2672

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• add flag to overwrite existing workspace so job doesn't error out when previous run was incomplete

  ChaochihL

  committed
  09bdc9d

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Commits on Dec 8, 2020

• add features to run on Slurm, cleanup some older code, and separate GATK 3 vs 4 functionality in some handlers

  ChaochihL

  committed
  42807ff

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Commits on Dec 3, 2020

• check for completion of time consuming step so it doesn't get re-run upon resubmission of job

  ChaochihL

  committed
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• haplotype caller fix handling of different parallelization options

  ChaochihL

  committed
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Commits on Nov 23, 2020

• add more useful message

  ChaochihL

  committed
  e2a37d7

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• clarify parallelizing across regions and chromosomes

  ChaochihL

  committed
  9e64e90

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• fix max array index setting when not parallelizing and add more informative message

  ChaochihL

  committed
  c335644

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• now handles gz vcf files too

  ChaochihL

  committed
  401b641

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• add option to reduce memory requirement

  ChaochihL

  committed
  df7ea3d

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• add GATK4 version of variant filtering and handle gz files

  ChaochihL

  committed
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Commits on Nov 21, 2020

• cleanup code

  ChaochihL

  committed
  d7a462a

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• allow user to choose queue to submit to

  ChaochihL

  committed
  05fa961

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Commits on Nov 5, 2020

• add option for sorting collection size ration, adds flexibility for dealing with core dump/out of memory issues

  ChaochihL

  committed
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• Merge branch 'master' of https://github.com/MorrellLAB/sequence_handling

  ChaochihL

  committed
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Commits on Nov 1, 2020

• add option and feature that resolves core dump/out of mem errors

  ChaochihL

  committed
  5c0b310

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Commits on Oct 21, 2020

• change name of commented out variables

  EDitt

  committed
  ebe44e5

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• formatting changes

  EDitt

  committed
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Commits on Oct 20, 2020

• rename file

  EDitt

  committed
  2a40da4

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• deal with decimals

  EDitt

  committed
  5853e33

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• Add interval info to filenames

  EDitt

  committed
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