Changes

Polymutt2 (view source)

581 bytes added , 23:32, 1 July 2015

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== Usage ==

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* First an LD pruned map file is generated by vcf2map. The following is the message by command vcf2map without any arguments

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Input : --vcf [], --ped [],

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--map [/scratch/cgg/lib13/db/hapmap/genetic_map_GRCh37_chr1.txt],

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--include_list [/scratch/cgg/Public/hg19/1000G.SNV.clean.MAF0.05.tbl.gz]

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Output : --out_map []

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Variant filter : --min_maf [0.10], --min_avg_dp [0.00],

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--max_avg_dp [-1.0e+00], --max_missing_rate [0.05]

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LD pruning : --win_size [100], --max_r2 [0.10], --ignore_missing

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* A command polymutt2 without any argument displays the following message

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