allcools allc

allcools allc

execute_command_and_return_markdown('allcools bam-to-allc -h')
$ 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)