cassiopeia.pp.filter_bam#
- cassiopeia.pp.filter_bam(bam_fp, output_directory, quality_threshold=10, n_threads=1)[source]#
Filter reads in a BAM that have low quality barcode or UMIs.
- Parameters:
- bam_fp
str
Input BAM filepath containing reads to filter.
- output_directory
str
The output directory where the filtered BAM will be written to. This directory must exist prior to calling this function.
- quality_threshold
int
(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
int
(default:1
) Number of threads to use. Defaults to 1.
- bam_fp
- Return type:
- Returns:
Path to filtered BAM