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rad_haplotyper

A program for building haplotypes from paired-end ddRAD tags

Synopsis

Usage: perl rad_haplotyper.pl -v vcffile -r reference [options]

Options:

-v, --vcffile
        VCF input file

-r, --reference
        Reference genome (FASTA format)

-s, --samples
        Individual samples to use in the analysis - can be used multiple
        times for multiple individuals [Default: All]

-u, --cutoff
        Excludes loci with more than the specified number of SNPs
        [Default: No filter]

-h, --hap_count
        Excludes loci with more than the specified number of haplotypes
        relative to number of SNPs. Excluding forces other than mutation
        (i.e. recombination) the maximum number of haplotypes should be
        one more than the number of SNPs at the locus. The value
        provided is the number of haplotypes allowed in excess of the
        number of SNPs, which allows that mechanisms other than mutation
        may have influenced the number of haplotypes in the population.
        [Default: 100]

-x, --threads
        Run in parallel across individuals with a specified number of
        threads

-n, --indels
        Includes indels that are the only polymorphism at the locus
        (tag)

-d, --depth
        Specify a depth of sampling reads for building haplotypes
        [Default: 20]

-m, --miss_cutoff
        Proportion of missing data cutoff for removing loci from the
        final output. For example, to keep only loci with successful
        haplotype builds in 95% of individuals, enter 0.95. [Default:
        0.9]

-mp, --max_paralog_inds
        Count cutoff for removing loci that are possible paralogs from
        the final output. The value is the maximum allowable number of
        individuals with more than the expected number of haplotypes
        [Default: No filter]

-ml, --max_low_cov_inds
        Count cutoff for removing loci with low coverage or genotyping
        errors from the final output. The value is the maximum allowable
        number of individuals with less than the expected number of
        haplotypes [Default: No filter]

-g, --genepop
        Writes a genepop file using haplotypes. Must provide the name of
        the genepop file.

-o, --vcfout
        Writes a VCF file that contains SNPs (unhaplotyped) and genotypes that were successfully built into haplotypes. Must provide the name of the VCF file.

-a, --ima
        Writes a IMa file using haplotypes. Must provide the name of the
        IMa file.

-p, --popmap
        Tab-separated file of individuals and their population
        designation, one per line (required for Genepop output)

-t, --tsvfile
        Writes a tsv file using haplotypes - for mapping crosses only.
        Must provide the name of the tsv file.

-p1, --parent1
        Parent 1 of the mapping cross (must be specified if writing a
        tsv file)

-p2, --parent2
        Parent 2 of the mapping cross (must be specified if writing a
        tsv file)

-e, --debug
        Output extra logs for debugging purposes

Dependencies

The following perl modules are required for running rad_haplotyper:

Vcf
Data::Dumper
Getopt::Long
Pod::Usage
Bio::DB::Sam
List::MoreUtils
Term::ProgressBar
Parallel::ForkManager