Command Line Interface¶
This page shows the MicroHapulator command line interface: how inputs and settings are specified for each subcommand.
NOTE: The MicroHapulator CLI is under Semantic Versioning. In brief, this means that every stable version of the MicroHapulator software is assigned a version number, and that any changes to the software's behavior or interface require the software version number to be updated in prescribed and predictable ways.
Haplotype calling¶
mhpl8r type¶
Perform haplotype calling
usage: mhpl8r type [-h] [-o FILE] [-b B] [-m M] tsv bam
Positional Arguments¶
- tsv
path of a TSV file containing marker metadata, specifically the offset of each SNP for every marker in the panel
- bam
path of a BAM file containing NGS reads aligned to marker reference sequences and sorted
Named Arguments¶
- -o, --out
write output to FILE; by default, output is written to the terminal (standard output)
- -b, --base-qual
minimum base quality (PHRED score) to be considered reliable for haplotype calling; by default B=10, corresponding to Q10, i.e., 90% probability that the base call is correct
- -m, --max-depth
maximum permitted read depth; by default M=1000000
mhpl8r filter¶
Apply static and/or dynamic thresholds to distinguish true and false haplotypes. Thresholds are applied to the haplotype read counts of a raw typing result. Static integer thresholds are commonly used as detection thresholds, below which any haplotype count is considered noise. Dynamic thresholds are commonly used as analytical thresholds and represent a percentage of the total read count at the marker, after any haplotypes failing a static threshold are discarded.
usage: mhpl8r filter [-h] [-o FILE] [-s ST] [-d DT] [-c FILE] result
Positional Arguments¶
- result
MicroHapulator typing result in JSON format
Named Arguments¶
- -o, --out
write output to FILE; by default, output is written to the terminal (standard output)
- -s, --static
global fixed read count threshold
- -d, --dynamic
global percentage of total read count; e.g. use --dynamic=0.02 to apply a 2% analytical threshold
- -c, --config
CSV file specifying marker-specific thresholds to override global thresholds; three required columns: 'Marker' for the marker name; 'Static' and 'Dynamic' for marker-specific thresholds
Analysis and interpretation¶
mhpl8r balance¶
Compute interlocus balance
usage: mhpl8r balance [-h] [-c FILE] [-D] input
Positional Arguments¶
- input
a typing result including haplotype counts in JSON format
Named Arguments¶
- -c, --csv
write read counts to FILE in CSV format
- -D, --no-discarded
do not included mapping but discarded reads in read counts; by default, reads that are mapped to the marker but discarded because they do not span all variants at the marker are included
mhpl8r contrib¶
Estimate the minimum number of DNA contributors to a suspected mixture
usage: mhpl8r contrib [-h] [-o FILE] result
Positional Arguments¶
- result
typing result in JSON format
Named Arguments¶
- -o, --out
write output to FILE; by default, output is written to the terminal (standard output)
mhpl8r prob¶
Compute a profile random match probability (RMP) or an RMP-based likelihood ratio (LR) test
usage: mhpl8r prob [-h] [-e ε] [-o FILE] freq profile1 [profile2]
Positional Arguments¶
- freq
population haplotype frequencies in tabular (TSV) format
- profile1
typing result or simulated genotype in JSON format
- profile2
typing result or simulated genotype in JSON format; optional
Named Arguments¶
- -e, --erate
rate of genotyping error; by default ε=0.001
- -o, --out
write output to FILE; by default, output is written to the terminal (standard output)
mhpl8r diff¶
Compare two profiles and determine the markers at which their genotypes differ
usage: mhpl8r diff [-h] [-o FILE] profile1 profile2
Positional Arguments¶
- profile1
typing result or simulated profile in JSON format
- profile2
typing result or simulated profile in JSON format
Named Arguments¶
- -o, --out
write output to "FILE"; by default, output is written to the terminal (standard output)
mhpl8r dist¶
Compute a simple Hamming distance between two profiles
usage: mhpl8r dist [-h] [-o FILE] profile1 profile2
Positional Arguments¶
- profile1
typing result or simulated profile in JSON format
- profile2
typing result or simulated profile in JSON format
Named Arguments¶
- -o, --out
write output to "FILE"; by default, output is written to the terminal (standard output)
mhpl8r contain¶
Perform a simple containment test
usage: mhpl8r contain [-h] [-o FILE] profile1 profile2
Positional Arguments¶
- profile1
simulated or inferred genotype profile in JSON format
- profile2
simulated or inferred genotype profile in JSON format
Named Arguments¶
- -o, --out
write output to "FILE"; by default, output is written to the terminal (standard output)
mhpl8r convert¶
Convert a typing result to a format compatible with probabilistic genotyping software applications
usage: mhpl8r convert [-h] [-o FILE] [--no-counts] [-f] result sample
Positional Arguments¶
- result
filtered MicroHapulator typing result in JSON format
- sample
sample name
Named Arguments¶
- -o, --out
write output to 'FILE'; by default, output is written to the terminal (standard output)
- --no-counts
do not include haplotype counts if you are interpreting your data with a semi-continuous probgen model such as LRMix Studio; by default, haplotype counts are included for interpretation with fully continuous probgen model such as EuroForMix
- -f, --fix-homo
duplicate a homozygous haplotype so that it is reported twice
Simulation¶
mhpl8r sim¶
Simulate a diploid genotype from the specified microhaplotype frequencies
usage: mhpl8r sim [-h] [-s INT] [-o FILE] [--haplo-seq FILE]
[--sequences FILE] [--markers FILE]
freq
Positional Arguments¶
- freq
population microhaplotype frequencies in tabular (tab separated) format
Named Arguments¶
- -s, --seed
seed for random number generator
- -o, --out
write simulated profile data in JSON format to FILE
- --haplo-seq
write simulated haplotype sequences in FASTA format to FILE
- --sequences
microhaplotype sequences in FASTA format; required if --haplo-seq enabled, ignored if not
- --markers
microhaplotype marker definitions in tabular (tab separated) format; required if --haplo-seq enabled, ignored if not
mhpl8r mix¶
Combine simulated profiles into a mock DNA mixture
usage: mhpl8r mix [-h] [-o FILE] profiles [profiles ...]
Positional Arguments¶
- profiles
simulated genotype profiles in JSON format
Named Arguments¶
- -o, --out
write output to "FILE"; by default, output is written to the terminal (standard output)
mhpl8r unite¶
Simulate the creation of a new profile from a mother and father
usage: mhpl8r unite [-h] [-o FILE] [-s INT] mom dad
Positional Arguments¶
- mom
simulated or inferred genotype in JSON format
- dad
simulated or inferred genotype in JSON format
Named Arguments¶
- -o, --out
write output to "FILE"; by default, output is written to the terminal (standard output)
- -s, --seed
seed for random number generator
mhpl8r seq¶
Simulate paired-end Illumina MiSeq sequencing of the given profile(s)
usage: mhpl8r seq [-h] [-o OUT [OUT ...]] [-n N] [-p P [P ...]]
[-s INT [INT ...]]
tsv refrseqs profiles [profiles ...]
Positional Arguments¶
- tsv
microhaplotype marker definitions in tabular (TSV) format
- refrseqs
microhaplotype reference sequences in FASTA format
- profiles
one or more simple or complex profiles (JSON files)
Named Arguments¶
- -o, --out
write simulated paired-end MiSeq reads in FASTQ format to the specified file(s); if one filename is provided, reads are interleaved and written to the file; if two filenames are provided, reads are written to paired files; by default, reads are interleaved and written to the terminal (standard output)
- -n, --num-reads
number of reads to simulate; default is 500000
- -p, --proportions
simulated mixture samples with multiple contributors at the specified proportions; by default even proportions are used
- -s, --seeds
seeds for random number generator, 1 per profile