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CORGi - COmplex Rearrangement analysis with Graph-search

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CORGi

CORGi requires Matplotlib, Bokeh, and local installations of BLAST, SAMTools, and optionally IGV.

python corgi.py \

  • -r reference.fa
  • -b input.bam
  • -c chromosome
  • -p start & end coordinates
  • -o outputDir/
  • --skip-igv skip IGV screenshot
  • --skip-bam skip read extraction

example: python corgi.py -r hg38.fa -b my.bam -c chr1 -p 1000 2000 -o myOut/

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