R script that converts from the output file format used by ms to the haps/sample file format.
The script removes any sites with multiple mutations.
If the input file contains more than one simulation, these get separated into "chromosomes".

Download the script.

 Rscript ms2haps.R infile.ms example nsites

infile.ms

Input filename with file extension.

example

Output filename withouth file extension.

nsites

(Optional) Number of simulated sites. Default value is 1. This is multiplied to the positions.

Output: example.haps, example.sample.

Prepares input files for Relate. The script will remove non-biallelic SNPs, flip haplotypes according to the ancestral genome such that the ancestral allele is always denoted by 0, remove samples if specified, filter SNPs and adjust distances between SNPs using a genomic mask if specified, and generate SNP annotations needed for some add-on modules.
See here for links to external resources, such as an ancestral genome.

--haps

Filename of .haps file.

--sample

Filename of .sample file

-o,--output

Filename of output files without file extensions. If same as input filenames, input files will be overwritten.

--ancestor

Fasta file containing ancestral genome. This is case insensitive.

--mask

Optional: Fasta file of same length as the ancestral genome containing a genomic mask. Loci passing the mask are denoted by P, loci not passing the mask are denoted by N. This is case insensitive.

--remove_ids

Optional: File containing ids of samples that will be removed from the haps/sample files. One id per line.

--poplabels

Optional: File containing population labels of samples.

 PATH_TO_RELATE/scripts/PrepareInputFiles/PrepareInputFiles.sh \
                 --haps example.haps \
                 --sample example.sample \
                 --ancestor ancestor.fa \
                 --mask mask.fa \
                 --remove_ids remove_ids.txt \
                 --poplabels example.poplabels
                 -o example_input 

Output: example_input.haps, example_input.sample, example_input.dist (if --mask if specified), example_input.poplabels (if remove_ids and poplabels is specified), example_input.annot (if poplabels is specified).

Removes SNPs that are not biallelic in the data set.

 PATH_TO_RELATE/bin/RelateFileFormats \
                 --mode RemoveNonBiallelicSNPs \
                 --haps example.haps \
                 -o example_biallelic 

Output: example_biallelic.haps.

The ancestral genome should be saved as a fasta file and aligned to the data set. The code is insensitive to case in the fasta file and deletes SNPs at which neither allele matches the ancestral allele.

 PATH_TO_RELATE/bin/RelateFileFormats \
                 --mode FlipHapsUsingAncestor \
                 --haps example.haps \
                 --sample example.sample \
                 --ancestor ancestor.fa \
                 -o example_ancestral 

Output: example_ancestral.haps

Write ids of individuals as specified in the .sample file into remove_ids.txt (one id per line). These indivduals will be removed from the data set. Argument --poplabels is optional. If specified, it will generate a new poplabels file for the subsetted samples.

 PATH_TO_RELATE/bin/RelateFileFormats \
                 --mode RemoveSamples \
                 --haps example.haps \
                 --sample example.sample \
                 --poplabels example.poplabels \
                 -i remove_ids.txt \
                 -o example_subset 

Output: example_subset.haps, example_subset.sample, example_subset.poplabels (if --poplabels is specified).

The genomic mask needs to be specified as a fasta file of same length as the ancestral genome, such that the xth entry is the xth base of the genome. The passing state should be denoted as P. The code is insensitive to case in the fasta file and deletes all SNPs that are not passing. It also outputs a .dist file that contains the distances between SNPs, adjusted for regions that are not passing in the mask.

 PATH_TO_RELATE/bin/RelateFileFormats \
                 --mode FilterHapsUsingMask\
                 --haps example.haps \
                 --sample example.sample \
                 --mask genomic_mask.fa \
                 -o example_mask 

Output: example_mask.haps, example_mask.dist.

This code uses the ancestral genome and population labels of samples to append additional information to the output of Relate. Fileformat for population labels is described here. The ancestral genome should be saved in fasta file format and aligned to the data set. Argument --ancestor is optional. If argument --mut is specified, output is directly appended to the .mut file.

 PATH_TO_RELATE/bin/RelateFileFormats \
                 --mode GenerateSNPAnnotations \
                 --haps example.haps \
                 --sample example.sample \
                 --poplabels example.poplabels \
                 --ancestor ancestor.fa \
                 -o example 

Output: example.annot. If --mut is specified, columns are appended to example.mut.

This function converts anc/mut files inferred by Relate into the tree sequence file format used by tskit. In the current implementation, each tree is stored with new nodes in the tree sequence file format, leading to no compression. In addition, information about how long branches persist, and how many mutations map to a branch are lost by this conversion.

-i,--input

Filename of .anc and .mut files without file extension.

-o,--output

Filename of the output tree sequence file without file extensions.

 PATH_TO_RELATE/bin/RelateFileFormats \
                 --mode ConvertToTreeSequence \
                 -i example \
                 -o example
                    

Output: example.trees.

Extracts a tree at a SNP of interest in newick format.

--anc

Filename of the .anc file.

--mut

Filename of the .mut file.

--bp_of_interest

Integer specfifying the BP position of interest

-o,--output

File of the output files without file extensions.

 PATH_TO_RELATE/bin/RelateExtract\
                 --mode TreeAtSNPAsNewick \
                 --anc example.anc \
                 --mut example.mut \
                 --bp_of_interest 3000000 \
                 -o example 

Output: example_at_.newick.