Hi all,
I am trying to do some GWAS which requires 1001 population Arabidopsis genotype and SNPs data to run FarmCPU (http://www.zzlab.net/FarmCPU/index.html). However, I have some issue in getting the 1001 Arabidopsis genotype and SNPs data that fits the FarmCPU. Therefore, I downloaded some .vcf.gz data and try to convert them into HapMap using vcftools. After the conversion, I have a .MAP file and a .PED file. I believe the .MAP file is the HapMap, but I don't understand what those columns represent in that file. I also do not know how to convert them into the genotype and SNPs data that I need. The genotype and SNPs data I need should look like this:
Data I downloaded and parsed:
https://1001genomes.org/data/GMI-MPI/releases/v3.1/1001genomes_snp-short-indel_only_ACGTN.vcf.gz
https://1001genomes.org/data/GMI-MPI/releases/v3.1/1001genomes_snp-short-indel_with_tair10_only_ACGTN.vcf.gz
