GitHub - sgusev/GERMLINE: Linear time detection of Identity by Descent

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Name		Name	Last commit message	Last commit date
Latest commit History 10 Commits
include		include
test		test
BasicDefinitions.h		BasicDefinitions.h
Chromosome.cpp		Chromosome.cpp
Chromosome.h		Chromosome.h
ChromosomeIndividualPair.h		ChromosomeIndividualPair.h
ChromosomePair.cpp		ChromosomePair.cpp
ChromosomePair.h		ChromosomePair.h
GERMLINE.cpp		GERMLINE.cpp
GERMLINE.h		GERMLINE.h
GERMLINE_0001.cpp		GERMLINE_0001.cpp
HMIndividualsExtractor.cpp		HMIndividualsExtractor.cpp
HMIndividualsExtractor.h		HMIndividualsExtractor.h
Individual.cpp		Individual.cpp
Individual.h		Individual.h
Individuals.cpp		Individuals.cpp
Individuals.h		Individuals.h
InputManager.cpp		InputManager.cpp
InputManager.h		InputManager.h
Makefile		Makefile
MarkerSet.cpp		MarkerSet.cpp
MarkerSet.h		MarkerSet.h
Match.cpp		Match.cpp
Match.h		Match.h
MatchFactory.cpp		MatchFactory.cpp
MatchFactory.h		MatchFactory.h
MatchesBuilder.cpp		MatchesBuilder.cpp
MatchesBuilder.h		MatchesBuilder.h
NucleotideMap.cpp		NucleotideMap.cpp
NucleotideMap.h		NucleotideMap.h
PEDIndividualsExtractor.cpp		PEDIndividualsExtractor.cpp
PEDIndividualsExtractor.h		PEDIndividualsExtractor.h
PolymorphicIndividualsExtractor.cpp		PolymorphicIndividualsExtractor.cpp
PolymorphicIndividualsExtractor.h		PolymorphicIndividualsExtractor.h
README		README
SNP.cpp		SNP.cpp
SNP.h		SNP.h
SNPPositionMap.cpp		SNPPositionMap.cpp
SNPPositionMap.h		SNPPositionMap.h
SNPs.cpp		SNPs.cpp
SNPs.h		SNPs.h
Share.cpp		Share.cpp
SharedSegmentPointer.h		SharedSegmentPointer.h
WindowInfo.cpp		WindowInfo.cpp
WindowsList.cpp		WindowsList.cpp
WindowsList.h		WindowsList.h
germline		germline
parse_bmatch.cpp		parse_bmatch.cpp

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GERMLINE
--------
http://www1.cs.columbia.edu/~gusev/germline/

# About
GERMLINE is a program for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing.

GERMLINE uses a novel hashing & extension algorithm which allows for segment identification in haplotype data in time proportional to the number of individuals. With genotype data, GERMLINE implements several pedigree-based phasing techniques to impute data for related individuals, and then iteratively uses identified IBD segments to infer additional missing information. GERMLINE can identify shared segments of any specified length, as well as allow for any number of mismatching markers.

The program has been developed in Itsik Pe'er's Lab of Computational Genetics at Columbia University. It is built in C++ and tested in the Red Hat Linux environment; the source is distributed here in a tar.gz package under the GPL license.

# Usage
Compile germline with make.
The executable is run as `germline <options>` which prompts the user for input/output file information and runs the algorithm.

# Input
GERMLINE accepts as input the following formats:

* Plink / ped+map
* PHASE / HapMap

GERMLINE also accepts an optional genetic map, formatted according to the HapMap standard described here ( http://ftp.hapmap.org/recombination/ ).

# Output
Upon completion, GERMLINE generates a .match file in the specified location. The first five lines contain meta-data detailing the run settings and executions time. The following rows detail the identified pairwise shared segments, one per row, with each row containing the following fields:

* Family ID 1
* Individual ID 1
* Family ID 2
* Individual ID 2
* Segment start (bp)
* Segment end (bp)
* Mismatching SNPs in segment
* Total SNPs in segment
* Genetic Length of segment(cM)