Input

1. Input vcf file (variant list)

Prepare sorted variants in vcf format. The INFO field in each entry includes a sample ID in SAMPLE={sample_id} format.

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
chr1    3747728 .        T       C       .       .       SAMPLE=11000.p1
chr1    38338861        .       C       A       .       .       SAMPLE=11000.p1
chr1    117942118       .      T       G       .       .       SAMPLE=11000.p1

2. Sample information

Prepare the sample information in a text file, such as in txt or tsv format. The file must be tab separated. It also must contain three columns, SAMPLE and PHENOTYPE. A value in the PHENOTYPE muse be case or ctrl. The values in the SAMPLE column are matched to the sample IDs of variants in the input vcf file.

SAMPLE	PHENOTYPE
11000.p1	case
11000.s1	ctrl
11002.p1	case
11002.s1	ctrl

3. Adjustment factors

Adjustment factors are required if the users want to adjust the number of variants for each sample in CWAS-Plus. The file must be tab separated and must contain two columns, SAMPLE and AdjustFactor. A value in the AdjustFactor must be a float. The values in the SAMPLE column must be matched to the sample IDs of variants in the input vcf file.

SAMPLE	AdjustFactor
11000.p1	0.932
11000.s1	1.082
11002.p1	0.895
11002.s1	1.113

For example run, the above data are available at joonan-lab/cwas-input-example.

cd $HOME
git clone https://github.com/joonan-lab/cwas-input-example.git