SR4R SnpReady for Rice

Description:

Extract hapmapSNPs genotype from the interested SNP set, when user provides a list of SNP positions in rice genome.

Usage:

perl extractTarHapmapPos.pl test2.snplist test2.hapmap > test2.output

Input file:

test2.snplist, test2.hapmap

Output files:

test2.output

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Description:

Extract flanking sequences from the interested SNP set, when user provides a list of SNP positions in rice genome. (for primer design)

Usage:

perl extractSNPflankSeq.pl ../SR4Rdatabase/IRGSP-1.0_genome.fasta test3.snplist 50 > test3.output

Input file:

IRGSP-1.0_genome.fasta, test3.snplist

Output files:

test3.output

Parameters:

flank-seq-length=[50/100/150/200/250]

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Description:

Convert a provided hapmap file to ped format.

Usage:

perl hapmap2plink.pl test4.hapmap ./test4.output

Input file:

test4.hapmap

Output files:

test4.output.ped, test4.output.map

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Description:

Convert a provided hapmap file to vcf format.

Usage:

perl hapmap2vcf.pl test5.hapmap > test5.vcf

Input file:

test5.hapmap

Output files:

test5.vcf

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Description:

Convert a provided hapmap file to bgl format.

Usage:

perl hapmap2beagle.pl test6.hapmap > test6.bgl

Input file:

test6.hapmap

Output files:

test6.bgl

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Description:

Imputation of missing genotype and phasing for a provided hapmap file (Please performed on each chromosome separately).

Usage:

perl ../1.6.hapmap2beagle/hapmap2beagle.pl test7.hapmap > test7.bgl

java -Xmx215180m -XX:MaxPermSize=215180m -jar beagle.jar unphased=test7.bgl missing=N out=test7.bgl

perl beaglephasedgz2hapmap.pl test7.hapmap test7.bgl.test7.bgl.phased.gz >test7.output.hapmap

Input file:

test7.hapmap

Output files:

test7.output.hapmap

Parameters:

missing=N

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