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* A VCF file [[http://www.1000genomes.org/node/101 VCF specs]]. It can contain variant information for more individuals than in the ped file.
* A VCF file [[http://www.1000genomes.org/node/101 VCF specs]]. It can contain variant information for more individuals than in the ped file.
** Note: In the VCF file either PL or GL has to be provided, and only the PL (or GL) field is used in the calling.
** Note: In the VCF file either PL or GL has to be provided, and only the PL (or GL) field is used in the calling.
* A map file in the PLINK format. See blow for examples how to generate a high quality map file.
== Examples of generating the map file ==
* vcf2map: generate a sparse map file (see [[#Download|Download]] for files genetic_map_GRCh37_chr1.txt and 1000G.SNV.clean.MAF0.05.tbl.gz)
vcf2map --vcf input.vcf --ped input.ped --map genetic_map_GRCh37_chr1.txt --include_list 1000G.SNV.clean.MAF0.05.tbl.gz --out_map chr1.map
* User defined r2 cutoff for LD pruning , min of average depth for filtering
vcf2map --vcf input.vcf --ped input.ped --map genetic_map_GRCh37_chr1.txt --include_list 1000G.SNV.clean.MAF0.05.tbl.gz --max_r2 0.2 --min_avg_dp 2 --out_map chr1.r0.2.map
== Output ==
== Output ==
