iLiner: a bioinformatics pipeline to perform identity-by-descent analysis
This repository contains the code for iLiner, a Python pipeline used to perform identity-by-descent (IBD) analysis using iLASH, as well as additionnal statistical calculations based on the output of iLASH.
Requirements / Dependencies
- Python v.3.5.0 or higher
- iLASH
- ...
Installation
iLiner is available as a pip package ans can be installed via:
git clone iliner
cd iliner
python iliner/iliner.py module [options]
Functionnality
iLiner consists of 3 main modules performing different functions:
- iLASH module: configures and runs iLASH
- IBD depth module: performs IBD depth calculation along the genome
- Stats module: performs statistical analysis on the output of iLASH, stratified by population
iLASH module
This module configures and runs the iLASH executable.
Usage with phased haplotype and sample files
Usage: iliner ilash [options]
Options:
-i, --ilash_path
Full path to the iLASH executable
-s, --sample
Sample file in PLINK format (see https://www.cog-genomics.org/plink2/formats#sample)
-hp, --haps
Phased haplotype file
(see http://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#hapsample)
-gm, --genetic_map
Genetic map file. The genetic map file should should share the same build as the sample file.
(see http://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#gmap)
-op, --outfile_prefix
Output file prefix
-ni, --no_indel
Optional argument, removes indels from the haplotype file.
Usage with a phased VCF file
Usage: iliner ilash [options]
Options:
-i, --ilash_path
Full path to the iLASH executable
-v, --vcf
Phased VCF file
-gm, --genetic_map
Genetic map file. The genetic map file should should share the same build as the sample file.
(see http://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#gmap)
-op, --outfile_prefix
Output file prefix
-ni, --no_indel
Optional argument, removes indels from the haplotype file.
Example usage with phased haplotype and sample files
TODO
Example usage with a phased VCF file
TODO
IBD depth module
This module performs IBD depth calculation along the genome and uses the output of the iLASH module.
Usage
Usage: iliner ibd_depth [options]
Options:
-mf, --mapfile
iLASH map file.
Space-separated.
Columns: Chromosome, rsID, GeneticPosition, PhysicalPosition
-io, --ilash_output
iLASH output file.
Tab-separated.
Columns: Person1, Hap1, Person2, Hap2, Chr, Start, Stop, SNP1, SNP2, IBD_Sharing, Measure
-op, --outfile_prefix
Output file prefix
Stats module
This module performs performs statistical analysis on the output of iLASH, stratified by population.
Usage
Usage: iliner stats [options]
Options:
-pf, --population_file
Population file.
Tab-separated.
Columns: Sample id, Population
-io, --ilash_output
iLASH output file.
Tab-separated.
Columns: Person1, Hap1, Person2, Hap2, Chr, Start, Stop, SNP1, SNP2, IBD_Sharing, Measure
-op, --outfile_prefix
Output file prefix