FamSeq specifications

Information


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

Versioning


No version available

Maintainer


  • person_outline Wenyi Wang

Publication for Family-based Sequencing program

FamSeq citations

 (2)
library_books

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

2014
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 […]

library_books

Using familial information for variant filtering in high throughput sequencing studies

2014
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 […]

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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