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AmpliconSuite / AmpliconSuite-pipeline

A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
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cnv_prefilter #42

Open uretaj opened 11 months ago

uretaj commented 11 months ago

If we are using our own bed file with CNV calls(not using CNVKit), do we need to call cnv_prefilter or is using amplified_intervals.py enough? What additional filtering does cnv_prefilter do?

jluebeck commented 11 months ago

Hi Jennifer - thanks for this question - yes, you will need the cnv_prefilter when giving your own calls.

The difference is this: cnv_prefilter.py - check if copy number gains are focal by comparing the copy number segment against the entire chromosome arm to see if it is significantly amplified above what the chromosome arm was called at. amplified_intervals.py - check that these regions of the genome are valid, and not low-complexity, repetitive elements.

If you run your copy number bed file through AmpliconSuite-pipeline.py (formerly PrepareAA.py) and do not set --run_AA and do not set --run_AC it will simply output a file called [sample]_AA_CNV_SEEDS.bed, which will be the focal amplification seed regions after all filters are applied. Hopefully there is no need to dissect the workflow and run the individual scripts in isolation.

Thanks, Jens

uretaj commented 11 months ago

thank you