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155 bytes added ,  23:30, 1 July 2015
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* NOTE: current version can only process one chromosome at a time
 
* NOTE: current version can only process one chromosome at a time
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== 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: 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
 
   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
  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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* User defined r2 cutoff for LD pruning , min of average depth for filtering
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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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== Examples of running polymutt2 ==
    
* polymutt2: taking a VCF and the map file generated by vcf2map (the vcf file can be a complete vcf with all variants and samples)
 
* polymutt2: taking a VCF and the map file generated by vcf2map (the vcf file can be a complete vcf with all variants and samples)
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