FastEPRR Version 1
Input Parameters
How to cite
[1] GAO Feng, MING Chen, HU Wangjie, LI Haipeng* (2016). New software for the fast estimation of population recombination rates (FastEPRR) in the genomic era. G3-Genes Genomes Genetics, 6(6): 1563-1571 [PMID=27172192]
[2] LIN Kao, FUTSCHIK Andreas, LI Haipeng* (2013). A fast estimate for the population recombination rate based on regression. Genetics 194:473-484 [PMID=23589457]
Help information

Version 1
Usage: -alnFilePath -format -erStart -erEnd -winLength_aln -stepLength_aln -vcf -winLength_step1 -stepLength_step1 -winDXThreshold -idvlConsidered -qualThreshold -gapFilePath -jobNumber -outputFilePath -outputName
-alnFilePath             Full path of the alignment file. The file name should end with [.fas|.aln|.phy|.txt]
-format                    1:fasta,2:clustal,3:phylip
-erStart                    A character value indicating the start position from which to estimate the

                                recombination rate.[NULL]
-erEnd                     A character value indicating the end position relative to erStart.[NULL]
-winLength_aln       The size of the sliding-window.[NULL]
-stepLength_aln      The length of the sliding step.[NULL]
-vcf                          Full path of vcf file. The file name shoule end with [.vcf|.gz], only one chromosome.
-winLength_step1   The size of the sliding-window.(kb)[NULL]
-stepLength_step1  The length of the sliding step.(kb)[winLength_step1]
-winDXThreshold     The minimum number of e2+ex for one window.[30]
-idvlConsidered       It indicates which individuals in the input are considered.(";")[all]
-qualThreshold        The threshold of quality.[20]
-gapFilePath            Full path of gap file. The gap file stores the gap information of the input chromosome,

                                and it has specified format.
-jobNumber             The number of jobs which are used to perform estimating in parallel.[1]
-outputFilePath       Full path of output file.
-outputName           Name of output file.

Parameters Description
-A: AlnFilePath
full path of the alignment file. The file name should end with [.fas|.aln|.phy|.txt]
-F: format
-S: ErStart
Full path of the alignment file. The file name should end with [.fas|.aln|.phy|.txt]
-E: ErEnd
A character value indicating the start position from which to estimate the recombination rate.
-WA: WinLength_aln
the size of the sliding-window.
-L: StepLength_aln
the length of the sliding step.
full path of vcf file. The file name shoule end with [.vcf|.gz], only one chromosome.
-WS: WinLength_step1
the size of the sliding-window.(kb)
-SL: StepLength_step1
the length of the sliding step.(kb)
-WT: WinDXThreshold
the minimum number of e2+ex for one window.
-I: IdvlConsidered
it indicates which individuals in the input are considered.(\ quot;;\ quot;)
-Q: QualThreshold
the threshold of quality .
-G: GapFilePath
full path of gap file. The gap file stores the gap information of the input chromosome, and it has specified format.
-J: JobNumber
the number of jobs which are used to perform estimating in parallel.
  • 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.