Introduction
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.
Version
Aug 14th, 2014. Please visit our new webpage here to download the latest FamSeq.
Reference
How to run FamSeq
1. download FamSeq source from http://odin.mdacc.tmc.edu/~wwang7/FamSeqIndex.html
2. extract files from the compressed file:
tar xvf FamSeq1.0.1.tar.gz
3. go to source file directory and compile the source file
cd FamSeq/src/
#CPU version
make
#GPU version if you have CUDA-enabled GPUs in your computer.
make -f makefile.gpu
#If you use MacOS 10.8 with XCode 5, or an error like "unsupported option '-dumpspecs'" occurs when compiling, use the following command to compile
make -f makefile.gpu.clang
4. run the test data
#CPU version
./FamSeq vcf -vcfFile ../TestData/test.vcf -pedFile ../TestData/PDF01.ped -output test.FamSeq.vcf -v
#GPU version
./FamSeqCuda vcf -vcfFile ../TestData/test.vcf -pedFile ../TestData/PDF01.ped -output test.FamSeq.vcf
Download CUDA for GPU programming
You can download the CUDA toolkit from here