Hapflk 2016

Introduction

hapflk is a software implementing the hapFLK ¹ and FLK ² tests for the detection of selection signatures based on multiple population genotyping data. ³

Installed version(s)

The following versions are installed and currently available...

... on environment hpc-env/8.3:

• hapflk/1.4-intel-2019b-Python-2.7.16

Loading / Using hapflk

To load the desired version of the module, use the module load command, e.g.

module load hpc-env/8.3
module load hapflk

Always remember: this commands are case sensitive!

To find out on how to use hapflk you can just type in hapflk -h after loading the module to print out a help text to get you started:

$ hapflk -h
usage: hapflk [-h] [--ped FILE] [--map FILE] [--file PREFIX] [--bfile PREFIX]
              [--miss_geno C] [--miss_pheno C] [--miss_parent C]
              [--miss_sex C] [--chr C] [--from x] [--to x] [--other_map]
              [-p PREFIX] [--ncpu N] [--eigen] [--reynolds] [--kinship FILE]
              [--reynolds-snps L] [--outgroup POP] [--keep-outgroup] [-K K]
              [--nfit NFIT] [--phased] [--kfrq] [--annot]

optional arguments:
  -h, --help            show this help message and exit
  -p PREFIX, --prefix PREFIX
                        prefix for output files (default: hapflk)
  --ncpu N              Use N processors when possible (default: 1)
  --eigen               Perform eigen decomposition of tests (default: False)
  --reynolds            Force writing down Reynolds distances (default: False)
  --annot               Shortcut for --eigen --reynolds --kfrq (default:
                        False)

Input Files:
  Available formats

  --ped FILE            PED file (default: None)
  --map FILE            MAP file (default: None)
  --file PREFIX         PLINK file prefix (ped,map) (default: None)
  --bfile PREFIX        PLINK bfile prefix (bim,fam,bed) (default: None)

Data format options:

  --miss_geno C         Missing Genotype Code (default: 0)
  --miss_pheno C        Missing Phenotype Code (default: -9)
  --miss_parent C       Missing Parent Code (default: 0)
  --miss_sex C          Missing Sex Code (default: 0)

SNP selection:
  Filter SNP by genome position

  --chr C               Select chromosome C (default: None)
  --from x              Select SNPs with position > x (in bp/cM) Warning :
                        does not work with BED files (default: 0)
  --to x                Select SNPs with position < x (in bp/cM) Warning :
                        does not work with BED files (default: inf)
  --other_map           Use alternative map (genetic/RH) (default: False)

Population kinship :
  Set parameters for getting the population kinship matrix

  --kinship FILE        Read population kinship from file (if None, kinship is
                        estimated) (default: None)
  --reynolds-snps L     Number of SNPs to use to estimate Reynolds distances
                        (default: 100000)
  --outgroup POP        Use population POP as outgroup for tree rooting (if
                        None, use midpoint rooting) (default: None)
  --keep-outgroup       Keep outgroup in population set (default: False)

hapFLK and LD model:
  Switch on hapFLK calculations and set parameters of the LD model

  -K K                  Set the number of clusters to K. hapFLK calculations
                        switched off if K<0 (default: -1)
  --nfit NFIT           Set the number of model fit to use (default: 20)
  --phased, --inbred    Haplotype data provided (default: False)
  --kfrq                Write Cluster frequencies (Big files) (default: False)

Documentation

The full documentation can be found here.