FARVAT beta as of April 21, 2014
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◎ Copyright (c) Sungkyoung Choi and Sungyoung Lee. All rights reserved.
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The current version of FARVAT release is beta version. A complete version of the software will be appearing soon.
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Instructions
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1. Input file
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1.1. Genotype data
: FARVAT support PLINK’s ped and binary format.
1.1.1 PED FILE
: The PED file is a white-space (tab or space) delimited file : the first six columns are mandatory:
Family ID Individual ID
Paternal ID (missing = 0)
Maternal ID (missing = 0)
Sex (male = 1, female = 2, missing = 0)
Phenotype (missing = -9 (default) )
1.1.2 MAP FILE
: Each line of the MAP file describes a single marker and must contain 4 columns:
Chromosome (1~22, 23 = X, 24 = Y) Marker ID or rs number
Genetic distance (Morgans)
Base-pair position (bp)
1.2. Phenotype data
: Sample lines of Phenotype and Covariates file. (tab or space delimited)
FID IID Pheno_1 Sex AGE 1 Ind1001 1 1 27 1 Ind1002 0 2 32 1 Ind1003 1 1 25 2 Ind2001 1 2 28
: The name of the marker set file which defines Gene sets. The first column of the file must be Gene ID, and the second column must be Marker ID.
GeneA 22:1000 GeneA 22:1001 GeneB 22:2000 GeneB 22:2100 GeneB 22:2110
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2. Create Kinship Coefficient Matrix or Genetic Relationship Matrix using FARVAT software. Make sure that ped and map (ped format) or bed, bim, and fam file (binary format) exist with the same prefix.
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2.1 Kinsip Coefficient Matrix
farvat --bed rare_test.bed --makecor --kinship # will generate res.theo.corfarvat --ped rare_test.bed --makecor --kinship # will generate res.theo.cor
2.2. Genetic Relationship Matrix
farvat --bed common_auto.bed --makecor # will generate res.empi.cofarvat --ped common_auto.ped --makecor # will generate res.empi.cor
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3. Run FARVAT with the ped/bed files, gene-marker set file, phenotype, and Kinship Coefficient Matrix / Genetic Relationship Matrix files as follows.
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farvat --bed rare_test.bed --set test.group --genetest --cor res.theo.cor --genesummary --mispheno -9 --out results_theo
farvat --ped rare_test.ped --set test.group --genetest --cor res.empi.cor --genesummary --sampvar test_pheno.txt --pname Pheno_1 --mispheno NA --out results_empi
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4. Output file
: This will generate the following files:
*[out_prefilx].gene.res : [CHR], [GENE], [NSAMP], [NVARIANT], [MAC], [P_BURDEN], [P_CALPHA], [P_SKATO], and so on.
CHR: Chromosome Number
GENE: Gene name
NSAMP: The number of samples
NVARIANT: The number of variants (SNPs)
MAC: The number of allele count
P_BURDEN: p-value of FARVATb
P_CALPHA: p-value of FARVATc
P_SKATO: p-value of FARVATo