$ allcools bam-to-allc -h
usage: allcools bam-to-allc [-h] --bam_path BAM_PATH --reference_fasta
REFERENCE_FASTA --output_path OUTPUT_PATH
[--cpu CPU] [--num_upstr_bases NUM_UPSTR_BASES]
[--num_downstr_bases NUM_DOWNSTR_BASES]
[--min_mapq MIN_MAPQ]
[--min_base_quality MIN_BASE_QUALITY]
[--compress_level COMPRESS_LEVEL]
[--save_count_df]
optional arguments:
-h, --help show this help message and exit
--cpu CPU Number of processes to use in parallel. DO NOT use cpu
> 1 for single cell ALLC generation. Parallel on cell
level is better for single cell project. (default: 1)
--num_upstr_bases NUM_UPSTR_BASES
Number of upstream base(s) of the C base to include in
ALLC context column, usually use 0 for normal BS-seq,
1 for NOMe-seq. (default: 0)
--num_downstr_bases NUM_DOWNSTR_BASES
Number of downstream base(s) of the C base to include
in ALLC context column, usually use 2 for both BS-seq
and NOMe-seq. (default: 2)
--min_mapq MIN_MAPQ Minimum MAPQ for a read being considered, samtools
mpileup parameter, see samtools documentation.
(default: 10)
--min_base_quality MIN_BASE_QUALITY
Minimum base quality for a base being considered,
samtools mpileup parameter, see samtools
documentation. (default: 20)
--compress_level COMPRESS_LEVEL
Compression level for the output file (default: 5)
--save_count_df If present, save an ALLC context count table next to
ALLC file. (default: False)
required arguments:
--bam_path BAM_PATH, -bam BAM_PATH
Path to 1 position sorted BAM file (default: None)
--reference_fasta REFERENCE_FASTA
Path to 1 genome reference FASTA file (the one used
for mapping), use samtools fadix to build .fai index
first. Do not compress that file. (default: None)
--output_path OUTPUT_PATH
Path to output ALLC file (default: None)
