- 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.
- 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
beforemake
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.
- for Ubuntu Linux, install
-
All executables will be created under the folder
bin/
Run them without parameter to see syntaxes.
Creates ab-genotype file from finalReport/affyInput file(s).
Merges ab-genotype files to a single ab-genotype file.
Trims the given ab-genotype file down on SNP names according to a 3-column (SNPName chr pos) map file.
Converts merged/unmerged ab-genotype files to VCF4.1 format, for imputation/phasing in beagle v4.
Converts phased/unphased, but must be imputed VCF4.1 file to merged/unmerged ab-genotype format.
Pipes a ab-genotype file to a new one, excluding animalIDs in the blackLisk file.
Converts the ab-genotype file to a -10/0/10 coded genotype file, replace missing data with column mean
To re-format ill-formatted finalReport files.
To group-replace according to a given cross-reference list file.
Group grep - greps lines from a target file acording to a given list file.
Proceed ab-genotype file to be a FImpute genotype file format. A snp_info.txt file is needed.
Unite 3-column
SNP_ID chr pos
map files to get a snp_info.txt genetic map file for FImpute.
Converts ab-genotype files with pedigree info and genetic map info to be imputable by findhap V3.
Converts findhap output to HapView input to make LD plots.
Converts findhap output to the format of FImpute (because SNPipeline toolset contains other tools to convert from FImpute)
Converts FImpute output file to ab-genotype file.
Converts FImpute output file to haplotype file.
Converts ab-genotype file to recoded (defined by a rule file) dense genotype matrix file.
Reads beagle v3 output files to generate files for doing SNPRelate PCA (matrix: 0-1-2 & SNP-in-row genotype files).
Reads beagle v3 output files to generate haplotype files (matrix: 0-1 & SNP-in-col & window-grouped haplotype files).
Reads beagle v4 phased output vcf format, converting to haplotype files.