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CHANGELOG.rst

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Changes for Munge

v3.4

  • specify polyhunter outfile with -o
  • specify CADD file from pipeline repo rather than parsing from annovar files
  • test for all variant types in varscan parser
  • update tests for monoseq/polyt
  • change polyt top-level to use samplesheet order for output order
  • change headers in polyt output
  • remove exception from xlsxmaker
  • update tests to ensure sorting of loadlist by well works
  • update code and tests to use manifest for sort order, get rid of exception in xlsxmaker
  • update for parsing correct number of controls in samplesheet creation

v3.3

  • test for all variant types in varscan parser
  • parse multiple calls at same position in genotyper, use qX depth

v3.8

  • munge annovar_summary updated
  • UW_DEC_p value included in SNP tab and top level output

v2.0.1

  • munge quality_metrics updated:
  • One quality parsing script works for hs metrics and/or quality metrics file
  • Print git version of pipeline in quality_analysis file
  • munge annovar_summary updated:
  • Add splice site effect prediction by AdaBoost and Random Forest from dbscSNV version 1.1
  • UW frequency now prints only for applicable assay-machine combo of sample
  • Variant_type is now a list of variant types
  • Use “--separate” flag to print all transcripts in annovar
  • Read count printed from gatk, varscan and varscanSNP, when available
  • munge amplicon_metrics added:
  • Print amplicon coverage metrics