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| --ld
| --ld
| Provide a file specifying LD between your reference SNP and all SNPs within the region you wish to plot. You only need to supply this file if you have created LD specifically for your purposes (perhaps a different population or genome build.) Otherwise, LD is computed automatically for you.
| Provide a file specifying LD between your reference SNP and all SNPs within the region you wish to plot. You only need to supply this file if you have created LD specifically for your purposes (perhaps a different population or genome build.) Otherwise, LD is computed automatically for you.
|-
| --ld-vcf
| Use a VCF file to calculate LD between SNPs. This can be a VCF file with an entire genome of SNPs and does not have to be subsetted to your region. The VCF file must also have a tabix index file. For calculating D', the VCF must be phased.
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| --source
| --source
