MARSweb

MARSweb is model-based method tool
that finds associations between variants
in risk loci and a phenotype, considering
the causal status of variants.

Upload Input files for MARSweb

You need a stat(Z-score) file and reference genome

Genotype + Stat LD + Stat Stat

Data description

--------- Genotype Data ---------
sample_geno
There is two fileds per variants variants_id counted_allele allelic dosage (0, 1, 2, NA for diploid variants)
ex) 3 variants 5samples file
         snp1 0 1 1 2 1
         snp2 1 1 2 1 2
         snp3 0 0 0 1 2

--------- Statistic Data ---------
sample_stat
The file in which Z-score are recorded according to the order of variables in the geno file
ex) 3 variants
         -0.547843
         -0.440051
           0.451124

The names of the geno file and stat file of the set to be analyzed must be the same.
ex) A_geno, A_stat, B_geno, B_stat

--------- LD Data ---------
sample_ld
The file containing a matrix representing the correlation between variants
ex) 3 variants file
          1    0.3  0.1
         0.3   1    0.2
         0.1  0.2   1

--------- Statistic Data ---------
sample_stat
The file in which Z-score are recorded according to the order of variables in the ld file
ex) 3 variants
         -0.547843
         -0.440051
           0.451124

The names of the ld file and stat file of the set to be analyzed must be the same.
ex) A_ld, A_stat, B_ld, B_stat

--------- Statistic file ---------

Produced by association test on a quantitative phenotype using plink(.qassoc).
The data columns required for analysis are CHR, SNP, BP, BETA, P.
Even in other types of summary statistic files,
there is no problem in analysis if only the values requested above are provided.
Fill other column values with 0.

--------- Set info Data ---------

A text file with a header line, and then one line per set info with chromosome number(chr), set_name, set position
ex) 2 set info
         chr set_name pos
         11    set1    200000
         21    set2   10000000

If you want to perform the analysis on your local computer, click here
MARSweb example dataset [Genotype + Stat] [LD + Stat]

MARSweb

MARSweb is model-based method tool that finds associations between variants in risk loci and a phenotype, considering the causal status of variants.

Upload Input files for MARSweb

You need a stat(Z-score) file and reference genome

MARSweb is model-based method tool
that finds associations between variants
in risk loci and a phenotype, considering
the causal status of variants.