Instructions

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
 
1.3. Set file (gene-marker set)

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.cor
farvat --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.co
farvat --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

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: 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

 

 

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