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, 18:06, 18 June 2014
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| This step prepares the reference panel by converting a VCF genotype file to a GENO file. We will skip this step and use a ready-to-use HGDP reference panel. A typical command to run the vcf2geno tool is given in the file "./LASER-2.01/vcf2geno/cmd.sh": | | This step prepares the reference panel by converting a VCF genotype file to a GENO file. We will skip this step and use a ready-to-use HGDP reference panel. A typical command to run the vcf2geno tool is given in the file "./LASER-2.01/vcf2geno/cmd.sh": |
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− | ./vcf2geno --inVcf exampleVCF/example.vcf.gz --updateID test.updateId --out test | + | # ./vcf2geno --inVcf exampleVCF/example.vcf.gz --updateID test.updateId --out test |
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| In the above command, -i specifies alternative IDs for the BAM files to be used in the .seq file (including popID and indivID). -b and -i are optional. | | In the above command, -i specifies alternative IDs for the BAM files to be used in the .seq file (including popID and indivID). -b and -i are optional. |
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| == Estimating ancestry coordinates using LASER == | | == Estimating ancestry coordinates using LASER == |