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, 12:38, 25 October 2016
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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. |
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| + | * 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 |
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| + | * 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 |
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| == Output == | | == Output == |