FamPipe is a NGS analysis pipeline for family data with complex diseases. FamPipe has many commonly used family analysis functions, such as identity-by-descent sharing among affected relatives, linkage analysis, imputation conditional on family structures, disease models, and family-based association tests. Several public resources, shown in the following table, are integrated in FamPipe.

Recent Update(2017/03/15): Docker image for FamPipe is available. Download the image and readme here.

Resource/Program Function
1000 Genomes Project Data Allele and haplotype frequency estimation
Rutger’s genetic map Haldane’s genetic map positions
PLINK2 File conversion
PedCut Split large pedigrees for Merlin
Merlin IBD sharing, linkage, and imputation analyses
GIGI+MORGAN Imputation analysis
FBAT Family-based association analysis
OVPDT Family-based association analysis


  • Please cite the FamPipe paper:
    Chung RH, Tsai WY, Kang CY, Yao PJ, Tsai HJ, Chen CH. 2016. FamPipe: An automatic analysis pipeline for analyzing sequencing data in families with complex diseases. PLOS Computational Biology. 12(6):e1004980.
Because different resources are integrated in FamPipe, please cite the corresponding papers if you performed analyses based on the following approaches:
  • PedCut:
    Liu, F., et al. An approach for cutting large and complex pedigrees for linkage analysis. European journal of human genetics : EJHG 2008;16(7):854-860.
  • Merlin:
    Abecasis, G.R., et al. Merlin--rapid analysis of dense genetic maps using sparse gene flow trees. Nature genetics 2002;30(1):97-101.
  • GIGI:
    Cheung, C.Y., et al. GIGI: an approach to effective imputation of dense genotypes on large pedigrees. American journal of human genetics 2013;92(4):504-516.
  • FBAT:
    De, G., et al. Rare variant analysis for family-based design. PloS one 2013;8(1):e48495.
  • OVPDT:
    Chung, R.H., et al. Family-based association test using both common and rare variants and accounting for directions of effects for sequencing data. PloS one 2014;9(9):e107800.
  • Segregation score:
    Koboldt, D.C., et al. Exome-based mapping and variant prioritization for inherited Mendelian disorders. American journal of human genetics 2014;94(3):373-384.
  • Compound heterozygosity filtering:
    Kamphans, T, et al. Filtering for compound heterozygous sequence variants in non-consanguineous pedigrees. PLoS One 2013; 8: e70151.
  • Weighted-sum statistics:
    Ionita-Laza, et al. Finding disease variants in Mendelian disorders by using sequence data: methods and applications. Am J Hum Genet 2011; 89: 701-712.