FamSeq statistics

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Citations per year

Number of citations per year for the bioinformatics software tool FamSeq

Tool usage distribution map

This map represents all the scientific publications referring to FamSeq per scientific context
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Associated diseases


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FamSeq specifications


Unique identifier OMICS_00058
Name FamSeq
Alternative name Family-based Sequencing program
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data FamSeq takes both likelihood and the widely used vcf files as input.
Input format VCF
Operating system Unix/Linux
Programming languages C++
Parallelization CUDA
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Wenyi Wang

Publication for Family-based Sequencing program

FamSeq citations


FamSeq: A Variant Calling Program for Family Based Sequencing Data Using Graphics Processing Units

PLoS Comput Biol
PMCID: 4214554
PMID: 25357123
DOI: 10.1371/journal.pcbi.1003880

[…] For variant calling using whole genome sequencing data, there are billions of loci. After filtering by FamSeq, there are still millions of candidate variant positions remaining; thus, we propose to parallelize the Bayesian network algorithm in order to reduce the computing time and make this approach f […]


Using familial information for variant filtering in high throughput sequencing studies

Hum Genet
PMCID: 4185103
PMID: 25129038
DOI: 10.1007/s00439-014-1479-4

[…] s. Furthermore, using a family-oriented HTS analysis pipeline can also produce Mendelian consistent genotype data from HTS data by making use of variant callers that incorporate familial information. FamSeq (Peng et al. ) and PolyMutt (Li et al. ) improve variant calling by making use of familial information while MATE-CLEVER (Marschall et al. ) performs family aware indel detection and calling. O […]

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FamSeq institution(s)
Department of Bioinformatics and Computational Biology, Division of Quantitative Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, CA, USA

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