downsample ¶

downsample(
    sample_id: str,
    r1: str,
    r2: str,
    out_path: str,
    reference: str,
    *,
    threads: int = 40,
    remove_all_dups: bool = False,
    remove_seq_dups: bool = False,
    use_gatk_md: bool = False,
    strategy: str = "HighAccuracy",
    keep: float = 0.5,
) -> None

Pipeline to map, deduplicate, and downsample sequencing reads.

Parameters:

Name	Type	Description	Default
`sample_id`	`str`	Sample ID.	required
`r1`	`str`	Path to R1 fastq file.	required
`r2`	`str`	Path to R2 fastq file.	required
`out_path`	`str`	Output path for the results.	required
`reference`	`str`	Path to the reference genome.	required
`threads`	`int`	Number of threads to use , default is 40.	`40`
`remove_all_dups`	`bool`	Whether to remove all duplicates, default is False.	`False`
`remove_seq_dups`	`bool`	Whether to remove sequencing duplicates, default is False.	`False`
`use_gatk_md`	`bool`	Whether to use Use GATK MarkDuplicatesSpark, default is False.	`False`
`strategy`	`str`	Downsampling strategy, default is 'High Accuracy'	`'HighAccuracy'`
`keep`	`float`	Ratio of the reads to keep [0-1], default is 0.5.	`0.5`