Software

Reference Coverage Profiles

We analyzed depth of coverage in over 6000 high quality (>40x) genomes. The depth of coverage has strong sequence-specific fluctuations only partially explained by global parameters like %GC.  To account for these fluctuations, we constructed multi-genome profiles representing the observed or inferred diploid depth of coverage at each position along the genome. These Reference Coverage Profiles (RCPs) take into account the diverse technologies and pipeline versions used.

Genetic Relationship by Averaged Blocks (GRAB) version 1.0

GRAB (Genetic Relationship by Averaged Blocks) is an algorithm for accurate estimation of genetic relationship from whole-genome data. GRAB segments the genome into blocks, calculates the fraction of blocks sharing identity, and then uses a parameter-based model to infer 1st- to 5th- degree relationships. It is 100% accurate for parent-offspring and full-siblings and >90% accurate for 2nd- to 3rd- degree and unrelated individuals.

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ISCA version 0.1.9

A new version of ISCA - v 0.1.9 - has been posted.  Updates to runISCA.pl, runISBProjs.pl, statistics_for_HMM_Suttonian_blocks.pl, and suttonian_hmm.pl

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ISCA Plotter

Software that creates a plot describing the different inheritance states in a family quartet.  When comparing the genomes of two siblings, there are four possible states of allele inheritance, depending on whether the children inherited the same alleles from both parents ("identical" state), share only a maternal allele or a paternal allele ("haploidentical maternal" or "haploidentical paternal", respectively), or share none ("nonidentical" state). Inheritance states are observed in large contiguous blocks: transitions between blocks correspond to recombinations.

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Painted Chromosome Figures

Software to draw a set of chromosomes with the ability to specify painted areas on the left side or right side to indicate regions of interest. In addition, specific gene positions can be called out in red.

KAVIAR

We present here Kaviar, a tool that greatly simplifies the assessment of novel variants. Kaviar includes: (i) an integrated and growing database of genomic variation from diverse sources, including over 55 million variants from personal genomes, family genomes, transcriptomes, SNV databases and population surveys; and (ii) software for querying the database efficiently.

Haploscribe

Haploscribe is a software package that uses Whole Genome Next Generation Sequencing data from a nuclear family to phase the genomic data into haplotypes spanning entire chromosomes.

ISCA

ISCA - Inheritance State Consistency Analysis software

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RepeatMasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program with the use of the default settings.

MAGMA: Multiobjective Analyzer for Genetic Marker Acquisition

MAGMA employs a multiobjective evolutionary algorithm to pick tag SNPs from a larger set of SNPs while balancing multiple objectives (e.g., cost and sensitivity). It is based on the ECJ evolutionary software package written by Sean Luke and includes the Strength Pareto Evolutionary Algorithm Version 2 changes for multiobjective analysis. The code runs on any platform with Java Version 2.

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