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--vcf [input.vcf.gz] --ped [input.ped (Optional)] --minAF 0.01 --minCallRate 0.95 \
--vcf [input.vcf.gz] --ped [input.ped (Optional)] --minAF 0.01 --minCallRate 0.95 \
--sepchr (if VCF is separated by chromosome) --out [outprefix.kinf] --run [# of parallel jobs]
--sepchr (if VCF is separated by chromosome) --out [outprefix.kinf] --run [# of parallel jobs]
If you provide [input.ped] file, then it will calculate the subset the individuals contained in the PED file.
The procedure above will create a file [outprefix.kinf] after splitting and merging the genomes into multiple pieces. If only a certain subset of SNPs needs to be considered due to target regions, LD-pruning, or any other reasons, a VCF containing the subset of markers must be created beforehand and should be used as input VCF file.
The procedure above will create a file [outprefix.kinf] after splitting and merging the genomes into multiple pieces. If only a certain subset of SNPs needs to be considered due to target regions, LD-pruning, or any other reasons, a VCF containing the subset of markers must be created beforehand and should be used as input VCF file.
