User options
Caleb Lareau
Quickly see all available modes, flags, and parameters using the following command:
mgatk --help
That should reveal a screen that looks like this:
Usage: mgatk [OPTIONS] [bcall|call|tenx|check|support]
mgatk: a mitochondrial genome analysis toolkit.
MODE = ['bcall', 'call', 'tenx', 'check', 'support']
See https://github.com/caleblareau/mgatk/wiki for more details.
Options:
--version Show the version and exit.
-i, --input TEXT Input; either directory of singular .bam
file; see documentation. REQUIRED.
[required]
-o, --output TEXT Output directory for analysis required for
`call` and `bcall`. Default = mgatk_out
-n, --name TEXT Prefix for project name. Default = mgatk
-g, --mito-genome TEXT mitochondrial genome configuration. Choose
hg19, hg38, mm10, (etc.) or a custom .fasta
file; see documentation. Default = rCRS.
[required]
-c, --ncores TEXT Number of cores to run the main job in
parallel.
--cluster TEXT Message to send to Snakemake to execute jobs
on cluster interface; see documentation.
--jobs TEXT Max number of jobs to be running
concurrently on the cluster interface.
-bt, --barcode-tag TEXT Read tag (generally two letters) to separate
single cells; valid and required only in
`bcall` mode.
-b, --barcodes TEXT File path to barcodes that will be
extracted; useful only in `bcall` mode. If
none supplied, mgatk will learn abundant
barcodes from the bam file (threshold
defined by the -mb tag).
-mb, --min-barcode-reads INTEGER
Minimum number of mitochondrial reads for a
barcode to be genotyped; useful only in
`bcall` mode; will not overwrite the
`--barcodes` logic. Default = 1000.
--NHmax INTEGER Maximum number of read alignments allowed as
governed by the NH flag. Default = 1.
--NMmax INTEGER Maximum number of paired mismatches allowed
represented by the NM/nM tags. Default = 4.
-kd, --keep-duplicates Retained dupliate (presumably PCR) reads
-ub, --umi-barcode TEXT Read tag (generally two letters) to specify
the UMI tag when removing duplicates for
genotyping.
-jm, --max-javamem TEXT Maximum memory for java for running
duplicate removal per core. Default = 8000m.
-pp, --proper-pairs Require reads to be properly paired.
-q, --base-qual INTEGER Minimum base quality for inclusion in the
genotype count. Default = 0.
-aq, --alignment-quality INTEGER
Minimum alignment quality to include read in
genotype. Default = 0.
-eb, --emit-base-qualities Output mean base quality per alt allele as
part of the final output.
-ns, --nsamples INTEGER The number of samples / cells to be
processed per iteration; Default = 7000.
Supply 0 to try all.
-k, --keep-samples TEXT Comma separated list of sample names to
keep; ALL (special string) by default.
Sample refers to basename of .bam file
-x, --ignore-samples TEXT Comma separated list of sample names to
ignore; NONE (special string) by default.
Sample refers to basename of .bam file
-z, --keep-temp-files Add this flag to keep all intermediate
files.
-qc, --keep-qc-bams Add this flag to keep the quality-controlled
bams after processing.
-sr, --skip-R Generate plain-text only output. Otherwise,
this generates a .rds obejct that can be
immediately read into R for downstream
analysis.
-so, --snake-stdout Write snakemake log to sdout rather than a
file. May be necessary for certain HPC
environments.
--help Show this message and exit.
