/SV_utils

Small utilities used in our SV pipeline

Primary LanguagePython

SV utils

Small utilities used in our SV calling pipeline

FilterSVByValue.py

Annotate SV VCF using any tab-separated file containing var ID and a float value

  • Positions of ID column and float value column are specified as arguments
  • Float value is annotated in INFO with the specified tag
  • A filter tag is added based on float value and max/min specified thresholds

Fix_svtools_VCF_.py

Fix formatting issues and float GQ values produced by svtool pipeline

  • Float GQ values are rounded to int
  • Dot values in sample fields are converted to zero
  • Poor variants lacking proper FORMAT fields are removed