--fasta hg_ref.fa ${reference_opt} \ | --fasta hg_ref.fa ${reference_opt} \ | ||||
--output-reference ${sample_id}.reference.cnn \ | --output-reference ${sample_id}.reference.cnn \ | ||||
--output-dir ./results/ \ | --output-dir ./results/ \ | ||||
--drop-low-coverage --diagram --scatter | |||||
--drop-low-coverage \ | |||||
--drop-outliers \ | |||||
--diagram --scatter | |||||
cp ${sample_id}.reference.cnn ~/${sample_id}.reference.cnn | cp ${sample_id}.reference.cnn ~/${sample_id}.reference.cnn | ||||