cassiopeia.pp.filter_bam

cassiopeia.pp.filter_bam(bam_fp, output_directory, quality_threshold=10, n_threads=1)

Filter reads in a BAM that have low quality barcode or UMIs.

Parameters

bam_fp : strstr

Input BAM filepath containing reads to filter.

output_directory : strstr

The output directory where the filtered BAM will be written to. This directory must exist prior to calling this function.

quality_threshold : intint (default: 10)

Every base of the barcode and UMI sequence for a given read must have at least this PHRED quality score for it to pass the filtering.

n_threads : intint (default: 1)

Number of threads to use. Defaults to 1.

Return type

strstr

Returns

Path to filtered BAM

cassiopeia.pp.error_correct_umis cassiopeia.pp.filter_molecule_table