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Revision as of 18:06, 18 June 2014
, 18:06, 18 June 2014→Preparing input files for LASER
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":
./vcf2geno --inVcf exampleVCF/example.vcf.gz --updateID test.updateId --out test
# ./vcf2geno --inVcf exampleVCF/example.vcf.gz --updateID test.updateId --out test
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.
== Estimating ancestry coordinates using LASER ==
== Estimating ancestry coordinates using LASER ==
