https://github.com/plantinformatics/durum_iselect_90ksnp_genotypecalling
Perl script for generating genotype calls for unrelated durum wheat samples assayed using the Illumina iSelect 90K SNP bead chip array
https://github.com/plantinformatics/durum_iselect_90ksnp_genotypecalling
Last synced: 3 months ago
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Perl script for generating genotype calls for unrelated durum wheat samples assayed using the Illumina iSelect 90K SNP bead chip array
- Host: GitHub
- URL: https://github.com/plantinformatics/durum_iselect_90ksnp_genotypecalling
- Owner: plantinformatics
- Created: 2018-08-27T04:36:36.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2018-08-27T04:49:50.000Z (almost 7 years ago)
- Last Synced: 2025-01-01T04:32:10.198Z (5 months ago)
- Language: Perl
- Size: 5.33 MB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# Durum_iSelect_90kSNP_GenotypeCalling
Perl script for generating genotype calls for unrelated durum wheat samples assayed using the Illumina iSelect 90K SNP bead chip array
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Call_90K_genotypes_For_Unrelated_Samples.pl
This scripts generates genotype calls for unrelated samples assayed using the iSelect 90K wheat SNP bead chip.
Genotype calls (A and B, where A denotes adenosine or thymine; and B denotes cytosine and guanine) are generated for
clusters that unambigiously associate with genetically map loci.
Options for running this perl script
-c Folder path and name of file containing cluster information; *_ClusterToMappedLoci.txt
-f Folder path and name of FullDataTable exported from GenomeStudio
Format: Text-delimited etc
-d Distance limit for cluster assignment (in standard deviations). Default 2
-s Confidence score for genotype call(value between 0 and 1, where 1 is highest) Default 0.7
-r Only report polymorphic SNPs in *_GENO_InformativeSNPtable and *_GENO_InformativeSNPreport
when they have MAF > user-specified value. Use 0 to report all SNPs
-o Folder path and name of output file
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