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DescriptionFamSeq is a computational tool for calculating probability of variants in family-based sequencing data
Development Information
GitHub wwylab/FamSeq
Current versionV1.0.2
PlatformsPlatform independent
LicenseGPL v3
Last updated07/01/2014
NewsVersion 1.0.2 includes option for GPU-based computing.
Citation Peng G., Fan Y., Palculict T.B., Shen P., Ruteshouser E.C., Chi A., Davis R.W., Huff V., Scharfe C., Wang W. Rare variant detection using family-based sequencing analysis. PNAS 110, p3985 (2013). 
Help and Support
Contact Wenyi Wang 


It is still challenging to call rare variants. In family-based sequencing studies, information from all family members should be utilized to more accurately identify new germline mutations. FamSeq serves this purpose by providing the probability of an individual carrying a variant given his/her entire family’s raw measurements. FamSeq accommodates de novo mutations and can perform variant calling at chrX.

FamSeq takes both likelihood and the widely used vcf files as input.


FamSeq V1.0.2

FamSeq V1.0.3

Updated in v1.0.3: Allows for VCF output from FreeBayes.

Build and Run

1. Extract files from the compressed file

tar xvf FamSeq1.0.2.tar.gz

For windows user, please check here to extract the file.

2. Build FamSeq

CPU version:

cd FamSeq/src/ 

GPU version:

cd FamSeq/src/
make -f makefile.gpu 

If you use MacOS 10.8 with XCode 5, or an error like “unsupported option ‘-dumpspecs’” occurs when compiling the GPU version, use the following command to compile

make -f makefile.gpu.clang

3. Run the test data

CPU version:

With VCF file as input:

./FamSeq vcf -vcfFile ../TestData/test.vcf -pedFile ../TestData/fam01.ped -output test.FamSeq.vcf -v

With likelihood only format file as input:

./FamSeq LK -lkFile ../TestData/loftest.txt -pedFile ../TestData/fam01.ped -output test.FamSeq.txt

GPU version:

With VCF file as input:

./FamSeqCuda vcf -vcfFile ../TestData/test.vcf -pedFile ../TestData/fam01.ped -output test.FamSeq.vcf -v

With likelihood only format file as input:

./FamSeqCuda LK -lkFile ../TestData/loftest.txt -pedFile ../TestData/fam01.ped -output test.FamSeq.txt



FamSeq vcf -vcfFile input.vcf -pedFile input.ped -output output.vcf
FamSeq LK -lkFile lk.txt -pedFile input.ped -output output.txt

Commands and Options

First specify the command according to the input file type. If the input file is a VCF file, the command is vcf. If it is a likelihood only format file, the command is LK.


FamSeq vcf [-method 1] [-mRate 1e-7] [-v] [-a]  [-l] [-vcfFile ] [-pedFile ] [-output] [-LRC] [-genoProbN] [-genoProbK] [-genoProbXN] [-genoProbXK] [numBurnIn] [numRep]



FamSeq LK [-method 1] [-mRate 1e-7] [-lkType n] [-v] [-a]  [-l] [-lkFile ]  [-pedFile ] [-output] [-LRC] [-genoProbN] [-genoProbK] [-genoProbXN] [-genoProbXK]



FamSeq creates a new file by adding three columns to the original input file as the output file: GPP, FPP and FGT. GPP is the posterior probability calculated by single individual based method and FPP is the posterior probability calculated by FamSeq. These probabilities are all Phred-scaled. FGT is the genotype called by FamSeq.