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Kevin Esoh edited this page Aug 6, 2019
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Merge single chromosomes into one file
./mergePlaf.sh <file> <output>
Update chromosome and snp IDs so that plink does not spill out errors
./updatePlafIDs.sh <merged-vcf>
Extract data for analysis as outlined above
./extract_data.sh <updated-vcf>
Phase extracted data with BEAGLE v5.0
./beaglePhase.sh <extracted-vcf> <output-prefix>
Convert phased haplotypes in VCF to rehh format (.hap+.map)
./phased_vcf2rehh.sh -h
Get help for using the script by typing '-h' on the commandline
Run scan for selection
./runScan.sh
Just hit 'enter' and the script will guide you through
Merge single chromosomes into one file
Update chromosome and snp IDs so that plink does not spill out errors
Extract data for analysis as outlined above
Phase extracted data with BEAGLE v5.0
Convert phased haplotypes in VCF to rehh format (.hap+.map)
Get help for using the script by typing '-h' on the commandline
Run scan for selection