hmmSweep Version 1
Inferring selection intensity and allele age through haplotype structure.
Input Parameters
How to cite
Chen H, Hey J, Slatkin M. A hidden Markov model for investigating recent positive selection through haplotype structure[J]. Theoretical Population Biology, 2015, 99(99C):18-30. [PMID=25446961]
Help information
hmmSweep

Version 1
Usage:
hmmSweep [arguments]
Inputs
-i     input hap file
-p    input position
-s     core set(example: 10,11,12)
options
-m    (int)min allele frequency for stopping expand(default:4)
-n     (int)haplotype number in one resample(defalult:100)
-f      (int)resample number in bootstrap(default:200);


Parameters Description
-I: Hap file
input hap file. For haplotype data, 1 234 represents A T G C (which can be mapped in different ways without affecting the calculation results). Each row represents a haplotype, and each column represents a locus. HAP file can calculate the location of the center, and take about 2Mb from top to bottom.
-P : Position file
input position
-S: Score set
the sequence numbers of allele age loci in all loci should be calculated. Core set can be a point or a continuous set of points. When the core set is a point, the calculation result is allele age of the point, and when the core set is a set of points, the calculation result is allele age of the point as a whole.
-M: Min allele freq
min allele frequency for stopping expand
-N: Haplotype number
haplotype number in one resample
-F: Resample number
resample number in bootstrap
  • Strategic Priority Research Program of the Chinese Academy of Sciences,Grant No. XDB13000000
    Maintained by BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences.