Plink/Seq on Helix
PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing projects, particularly whole-exome and whole-genome studies. However, the library could in principle be applied to other types of genetic studies, including whole-genome association studies of common SNPs.Plink/Seq was developed at Harvard University
How To Use
The plinkseq executables need to be added to your PATH environment variable before running the program. The easiest way to do this is by typing 'module load plinkseq' as in the example below.
helix% module load plinkseq helix% pseq ex1.vcf v-view --vmeta --gmeta chr1:1001 rs1001 T/C . 1 PASS . VM=1;SM=100 P001 1 C/C [GM=1] P002 1 T/T [GM=2] P003 1 T/C [GM=3] P004 1 C/C [GM=4] [...etc...]