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abyzovlab / CNVpytor

a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads
MIT License
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CRAM input #190

Closed gevro closed 1 year ago

gevro commented 1 year ago

Hi, Can CNVpytor handle CRAM input?

arpanda commented 1 year ago

CRAM input is supported, but you'll need to provide a fasta input reference file. To perform the 'rd' step, use the given usage command.

cnvpytor -root file.pytor -rd file.bam --reference_filename [path to fasta reference]

Thanks Arijit