Tool set for converting AB genotype calls from Illumina BeadExpress FinalReport format files or Affymetrix genotype files into various formats for genomic prediction, imputation/phasing or building haplotypes.
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SNPipeline.VCF2AB
SNPipeline.abg2bin
SNPipeline.abgExcl
SNPipeline.trimDown2Map
abg2FImpute
abg2M
abg2findhap
bin
bout2genotype
example
finalReportReformer
fout2abg
fout2haplotype
gReplace
ggrep
mapUniter
obj
.gitignore
.travis.yml
COPYING.LGPL
LICENSE
Makefile
README.md
RETIRED_CODE.h
SNP.h
SNPipeline.cpp
SNPipeline.mergingAB.cpp
SNPipeline_pooledAB2VCF41.cpp
affyInput.cpp
affyInput.h
appInfo.h
data.cpp
data.h
finalReport.cpp
finalReport.h
logger.cpp
logger.h
make.sh
splitablestring.h

README.md

SNPipeline Build Status

  • Tool set for converting AB genotype calls from Illumina BeadExpress FinalReport format files or Affymetrix genotype files into a simpler "one row per animal" format, namely ab-genotype file.

  • Tool set for converting ab-genotype files to appropriate format for genomic selection tool GenSel.

  • Tool set for converting ab-genotype files to appropriate format for imputation/phasing tools Beagle v3/v4, FImpute, and findhap.

  • Tool set for converting imputed or phased output files from Beagle v3/v4, FImpute, findhap back to ab-genotype files, or combining with map position info to create haplotype files.

  • Incorporated into BOLT software package since version 1.1.6 (Credit goes to Dorian and Bruce for making detailed documentations)

Compile

  • Just cd into the folder and execute
make

or

make -j8

may use 8 cores to run in parallel

  • Notice that SNPipeline.abg2bin depends on eigen, but other tools won't be affected if not installed.

    • for Ubuntu Linux, install libeigen3-dev before make
    sudo apt-get update && sudo apt-get install libeigen3-dev
    
    • for Mac OS X, I used port:
    sudo port install eigen3
    
    • Makefile may need to be modified for different systems.
  • All executables will be created under the folder

bin/

Executables

Run them without parameter to see syntaxes.

SNPipeline

Creates ab-genotype file from finalReport/affyInput file(s).

SNPipeline.mergingAB

Merges ab-genotype files to a single ab-genotype file.

SNPipeline.trimDown2Map

Trims the given ab-genotype file down on SNP names according to a 3-column (SNPName chr pos) map file.

SNPipeline.pooledAB2VCF41

Converts merged/unmerged ab-genotype files to VCF4.1 format, for imputation/phasing in beagle v4.

SNPipeline.VCF2AB

Converts phased/unphased, but must be imputed VCF4.1 file to merged/unmerged ab-genotype format.

SNPipeline.abgExcl

Pipes a ab-genotype file to a new one, excluding animalIDs in the blackLisk file.

SNPipeline.abg2bin

Converts the ab-genotype file to a -10/0/10 coded genotype file, replace missing data with column mean

finalReportReformer

To re-format ill-formatted finalReport files.

gReplace

To group-replace according to a given cross-reference list file.

ggrep

Group grep - greps lines from a target file acording to a given list file.

abg2FImpute

Proceed ab-genotype file to be a FImpute genotype file format. A snp_info.txt file is needed.

mapUniter

Unite 3-column SNP_ID chr pos map files to get a snp_info.txt genetic map file for FImpute.

abg2findhap

Converts ab-genotype files with pedigree info and genetic map info to be imputable by findhap V3.

fhout2hapview

Converts findhap output to HapView input to make LD plots.

fhout2fiout

Converts findhap output to the format of FImpute (because SNPipeline toolset contains other tools to convert from FImpute)

fout2abg

Converts FImpute output file to ab-genotype file.

fout2haplotype

Converts FImpute output file to haplotype file.

abg2M

Converts ab-genotype file to recoded (defined by a rule file) dense genotype matrix file.

bout2genotype

Reads beagle v3 output files to generate files for doing SNPRelate PCA (matrix: 0-1-2 & SNP-in-row genotype files).

bout2haplotype

Reads beagle v3 output files to generate haplotype files (matrix: 0-1 & SNP-in-col & window-grouped haplotype files).

vcf2haplotype

Reads beagle v4 phased output vcf format, converting to haplotype files.