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Diao Shuqi reported a bug in
gear.subcommands.CommandArguments.setPhenotypeIndex(String[] pheIndex)

the problem is that I incorrectly wrote "this.mPheno[i]--;"
I've removed it now.

see this commit.

I do eigengwas analysis for my wheat population. The population included two subgroup.

The commond is jar gear.jar eigengwas --bfile MCC_genotype_filter2 --inbred --ev 2 --out wheat125

The result included two files wheat125.1.egwas and wheat125.1.egwas.

Could you tell me which file is right?

Dear all,

I wonder if I can run EigenGWAS when I have more than ten groups. Thank you.

Best wishes,
Zheng zhuqing

Hi there,
When I try to compute Fst using GEAR, I found there is no RAF_SE columns in my GWAS summary statistics and in 1KG reference panel frq.file.
How can I get RAF_SE columns? Should I sample the GWAS SNPs matched to the 1KG reference samples?
I'm not really sure what is going on. Thank you in advance for your help!

--m Specify the number of markers for generating similarity scores between individuals. It defaults to use all markers.
but It defaults to use 100 markers……

--low-cutoff/--l

Specify the lower bounder for similarity cutoff. Only the similarity score lower than the given cutoff will be printed out.

--high-cutoff/--h

Specify the upper bounder for similarity cutoff. Only the similarity score lower higher than the given cutoff will be printed out.

Dear developers,

I am trying to run "java -jar gear.jar lam --meta-batch sum_stat_files.txt --qt-size sum_stat_size.txt --out test" on two summary stats files to see if there are overlapping samples.

The header of the first file is:
CHR SNP BP A1 A2 OR SE P
And the header of the second is:
CHR SNP BP A1 A2 BETA SE P

When I run the command I get:

[INFO]
[INFO] The keyword for 'SNP' is set to snp
[INFO] The keyword for 'BETA' is set to beta
[INFO] The keyword for 'SE' is set to se
[INFO] The keyword for 'A1' (reference allele) is set to a1
[INFO] The keyword for 'A2' (the other allele) is set to a2
[INFO] The keyword for 'CHR' is set to chr

[INFO] 2 cohorts are remained for analysis.

[INFO] Cannot find the beta/or column in SCZvsCONT_new.sumstats
[INFO] GEAR quit.

Can you please help me with that?

Two reset methods are needed.

1. reset() to the very beginning of the genotype stream
2. rollback(k) k individuals.

Columns order in the manual

Columns order my result

which is right?