GIST 0.3 – Detect Association between Marker Genotypes and IBD sharing at the same locus

GIST 0.3

:: DESCRIPTION

The GIST (Genotype-IBD Sharing Test) is a method for detecting association between marker genotypes and IBD sharing at the same locus.  Such an association will indicate that the marker itself, or one in linkage disequilibrium with it, could account for the observed linkage signal (at least partially).  The software can be used to analyze affected sibship data.

::DEVELOPER

Chun Li

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/Windows

:: DOWNLOAD

GIST

:: MORE INFORMATION

Citation

Li C, Scott LJ, Boehnke M. (2004)
Assessing Whether an Allele Can Account in Part for a Linkage Signal: The Genotype-IBD Sharing Test (GIST).
Am. J. Hum. Genet. 74:418-431

CYNTENATOR 20101005 – Progressive Gene Order Alignment of 17 Vertebrate Genomes

CYNTENATOR 20101005

:: DESCRIPTION

CYNTENATOR is a progressive gene order alignment software to identify genomic regions of conserved synteny over a large set of diverging species. CYNTENATOR does not depend on nucleotide-level alignments and a priori homology assignment.

::DEVELOPER

Dieterich lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CYNTENATOR

:: MORE INFORMATION

Citation:

PLoS One. 2010 Jan 28;5(1):e8861.
CYNTENATOR: progressive gene order alignment of 17 vertebrate genomes.
Rödelsperger  C, Dieterich C.

CDS-plotcon – Detect Enhanced Conservation in Coding Sequences

CDS-plotcon

:: DESCRIPTION

The software package CDS-plotcon is specifically designed to search for conserved functional elements within CDSs. It uses an average model of the expected mutation patterns within CDSs (incorporating a nucleotide mutation matrix, amino acid substitution matrix, sequence divergence parameter t, mean synonymous:nonsynonymous substitution ratio V and phylogenetic tree; it can handle up to three overlapping CDSs in different read-frames). Using this, it calculates the expected number of mutations across the alignment in each column and compares this with the observed number of mutations. The results are plotted along the genome, and optionally passed through a sliding window (clipped) mean filter

::DEVELOPER

Andrew Firth

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 CDS-plotcon

:: MORE INFORMATION

ATOM – Association Test via Optimally-weighted Markers

ATOM

:: DESCRIPTION

ATOM is a software of powerful gene-based Association Test by combining Optimally Weighted Markers within a genomic region. Due to variation in linkage disequilibrium, different markers often associate with the trait of interest at different levels.

::DEVELOPER

Chun Li, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ATOM

:: MORE INFORMATION

Citation

Li M, Wang K, Grant SF, Hakonarson H, Li C (2009)
ATOM: A powerful gene-based association test by combining optimally weighted markers.
Bioinformatics 25:497-503 (PMID: 19074959)

 

LOCO-LD – LOcalization COrrected for Linkage Disequilibrium

LOCO-LD

:: DESCRIPTION

LOCO-LD is a method for the geographic localization of individuals. It takes as input genotype data and generates, for each individual, an estimate for their geographic coordinates of origin.

::DEVELOPER

Bogdan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • C Compiler
  • Matlab

:: DOWNLOAD

 LOCO-LD

:: MORE INFORMATION

Citation:

Enhanced Localization of Genetic Samples through Linkage-Disequilibrium Correction
Yael Baran, Inés Quintela, ángel Carracedo, Bogdan Pasaniuc, Eran Halperin
The American Journal of Human Genetics – 6 June 2013 (Vol. 92, Issue 6, pp. 882-894)

SampleSeq and SampleSeq2 – Optimal Subject Selection in Targeted and Whole Genome Sequencing Experiments

SampleSeq and SampleSeq2

:: DESCRIPTION

SampleSeq is a probability-based algorithm for selecting samples for a targeted resequencing experiment.

SampleSeq2 requires a squared matrix of pairwise distance among all subjects that are candidates for selection. The matrix can be generated by PLINK using GWAS data or by Idcoefs using pedigree information. These are explained in detail in Sections II and III.In Section IV, we describe how to use SampleSeq2 for subject selection. In Section V, we describe how to estimate the number of independent genomes in a subset of subjects.

::DEVELOPER

Chun Li, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SampleSeq

:: MORE INFORMATION

Citation

Edwards TL, Li C (2012)
Optimized selection of unrelated subjects for whole genome sequencing studies of rare high-penetrance alleles.
Genet Epidemiol. 2012 Jul;36(5):472-9. doi: 10.1002/gepi.21641. Epub 2012 May 23.

 

GWAsimulator 2.1 – Rapid Whole Genome Simulation program

GWAsimulator 2.1

:: DESCRIPTION

GWAsimulator is a C++ program that can simulate genotype data for SNP chips that are used in genome-wide association (GWA) studies. It implements a rapid moving-window algorithm (Durrant et al. 2004. AJHG 75:35-43) to simulate whole genome case-control or population samples. It also can simulate specific regions if desired. For case-control data, the program retrospectively sample cases and controls according to a user-specified multi-locus disease model. The program requires phased data as input, and the simulated data will have similar LD patterns as the input data.

::DEVELOPER

Chun Li, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

  GWAsimulator

:: MORE INFORMATION

Citation

Li C, Li M (2008)
GWAsimulator: A rapid whole genome simulation program.
Bioinformatics 24:140-142

 

LDlink / LDlinkR 1.1.2 – Linkage Disequilibrium in Population group

LDlink / LDlinkR 1.1.2

:: DESCRIPTION

LDlink is a suite of web-based applications designed to easily and efficiently interrogate linkage disequilibrium in population groups.

LDhap: Calculate population specific haplotype frequencies of all haplotypes observed for a list of query SNPs. Input is a list of SNP RS numbers (one per line) and a population group.

LDmatrix: Create an interactive heatmap matrix of pairwise linkage disequilibrium statistics. Input is a list of SNP RS numbers (one per line) and a population group.

LDpair: Investigate correlated alleles for a pair of SNPs in high LD. Input is two RS numbers and a population group.

LDproxy: Interactively explore proxy and putatively functional SNPs for a query SNP. Input is an RS number and a population group.

::DEVELOPER

Mitchell Machiela in collaboration with NCI’s Center for Biomedical Informatics and Information Technology (CBIIT).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser
  • R

:: DOWNLOAD

LDlinkR

:: MORE INFORMATION

Citation

LDlink: A web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants.
Machiela MJ, Chanock SJ.
Bioinformatics. 2015 Jul 2. pii: btv402.

MIXSCORE 1.3 – Disease Scoring in Admixed Populations

MIXSCORE 1.3

:: DESCRIPTION

MIXSCORE is a software for disease scoring (combining case-only admixture and case-control SNP association signals) in Admixed Populations such as African Americans.

::DEVELOPER

Bogdan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MIXSCORE

:: MORE INFORMATION

Citation:

Pasaniuc et al. (2011).
Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a breast cancer consortium.
PLoS Genet. 2011 Apr;7(4):e1001371.

Lanc-CSV 0.1 – Local Ancestry Inference using Continental Specific Variants

Lanc-CSV 0.1

:: DESCRIPTION

Lanc-CSV is a method that uses continental-specific variants (i.e. variants present in individuals from only one continental group such as Europeans or Africans) for accurate local ancestry inference.

::DEVELOPER

Bogdan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • C++ / Matlab

:: DOWNLOAD

  Lanc-CSV

:: MORE INFORMATION

Citation:

PLoS Comput Biol. 2014 Apr 17;10(4):e1003555. doi: 10.1371/journal.pcbi.1003555. eCollection 2014.
Enhanced methods for local ancestry assignment in sequenced admixed individuals.
Brown R1, Pasaniuc B