Command Line Interface

mutyper: ancestral kmer mutation types for variant data

usage: mutyper [-h] {ancestor,variants,targets,spectra,ksfs} ...

Sub-commands

ancestor

create an ancestral FASTA file, using an outgroup alignment, and a database of SNPs with a callability mask

mutyper ancestor [-h] [--verbose] [--bed BED]
                 vcf reference outgroup chain output

Positional Arguments

vcf: VCF/BCF file, usually for a single chromosome (“-” for stdin)
reference: path to reference FASTA for one chromosome
outgroup: path to outgroup genome FASTA
chain: path to alignment chain file (reference to outgroup)
output: path for output ancestral FASTA for this chromosome

Named Arguments

--verbose: increase logging verbosity
--bed: path to BED file mask (“-” for stdin)

variants

adds mutation_type to VCF/BCF INFO, polarizes REF/ALT/AC according to ancestral/derived states, and stream to stdout

mutyper variants [-h] [--verbose] [--k K] [--target TARGET] [--sep SEP]
                 [--chrom_pos CHROM_POS] [--strand_file STRAND_FILE]
                 [--strict]
                 fasta vcf

Positional Arguments

fasta: path to ancestral FASTA
vcf: VCF/BCF file, usually for a single chromosome (“-” for stdin)

Named Arguments

--verbose: increase logging verbosity
--k: k-mer context size (default 3)
--target: 0-based mutation target position in kmer (default middle)
--sep: field delimiter in FASTA headers (default “:”)
--chrom_pos: 0-based chromosome field position in FASTA headers (default 0)
--strand_file: path to bed file with regions where reverse strand defines mutation context, e.g. direction of replication or transcription (default collapse reverse complements)
--strict: only uppercase nucleotides in FASTA considered ancestrally identified

targets

compute 𝑘-mer target sizes and stream to stdout

mutyper targets [-h] [--verbose] [--k K] [--target TARGET] [--sep SEP]
                [--chrom_pos CHROM_POS] [--strand_file STRAND_FILE] [--strict]
                [--bed BED]
                fasta

Positional Arguments

fasta: path to ancestral FASTA

Named Arguments

--verbose: increase logging verbosity
--k: k-mer context size (default 3)
--target: 0-based mutation target position in kmer (default middle)
--sep: field delimiter in FASTA headers (default “:”)
--chrom_pos: 0-based chromosome field position in FASTA headers (default 0)
--strand_file: path to bed file with regions where reverse strand defines mutation context, e.g. direction of replication or transcription (default collapse reverse complements)
--strict: only uppercase nucleotides in FASTA considered ancestrally identified
--bed: path to BED file mask (“-” for stdin)

spectra

compute mutation spectra for each sample in VCF/BCF with mutation_type data and stream to stdout

mutyper spectra [-h] [--verbose] [--population] [--randomize] vcf

Positional Arguments

vcf: VCF/BCF file, usually for a single chromosome (“-” for stdin)

Named Arguments

--verbose: increase logging verbosity
--population: population-wise spectrum, instead of individual
--randomize: randomly assign mutation to a single haplotype

ksfs

compute sample frequency spectrum for each mutation type from a VCF/BCF file with mutation_type data (i.e. output from variants subcommand ) and stream to stdout

mutyper ksfs [-h] [--verbose] vcf

Positional Arguments

vcf: VCF/BCF file, usually for a single chromosome (“-” for stdin)

Named Arguments

--verbose: increase logging verbosity