A collection of codes designed to process a range of basic, large-scale analyses for SNPs of maize diversity panel.
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README.md

zmSNPtools

A collection of python, perl and R codes designed to process a range of basic,
large-scale analyses for SNPs of maize diversity panel.

Usage:

Copy the piece of python code to the directory in your $PATH: for example:

$: cp impute4diallel/impute4diallel.py ~/bin/impute4diallel

Then, you will be ready to run it

# to find the help:
$: impute4diallel -help

Description

fpSNP

find a set of population specific fingerprint SNPs

update of the program

10/3/2014: v0.1 python code tested with a small set of simulated data

usage:

git clone git@github.com:yangjl/zmSNPtools.git
cd to/your/path
cp zmSNPtools/packages/fpSNP/fpSNP_v0.1.py zmSNPtools/bin/fpSNP
chmod +x zmSNPtools/bin/fpSNP
export PATH=$PATH:full/path/of/zmSNPtools/bin/
fpSNP -h

gerpIBD

Compute the GERP score in a given IBM regions across different genotypes.

update of the program

12/17/2014: beta version for testing run

impute4diallel

SNP Imputation for maize diallel population from parental SNP panel to F1 hybrids.

dsf2GWAS

transform density SNP format (DSF) to GWAS (gensel4.2 supported) and other formats

top2ref.pl

translate illumina top/bot SNP call to ref/alt based on the reference genome.

usage:

##cloned from: https://github.com/VertebrateResequencing/vr-codebase
##The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute
# added perl module
export PERL5LIB=$PERL5LIB:~/Documents/Github/zmSNPtools/modules
cp packages/top2ref/top2ref.pl bin/top2ref
# use samtools to index reference genome in fasta format
sed -i -- 's/chromosome:AGPv2:.*chromosome /chr/g' ZmB73_RefGen_v2.fasta
samtools faidx ZmB73_RefGen_v2.fasta

cat snps.top | topbot-to-fwd-strand -r ref.fa > snps.map 

Update

General

  1. changed gitignore
  2. unwatch the MyPack and test folders

packages:

  1. updated a SNP merge package snp3merge: merge hapmap1, hapmap2 and RNA-seq data
  2. updated impute4diallel
  3. updated snpfrq
  4. updated merge4ames

MyPack

  1. updated and tested snp_sampling program for XBSA project;