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/