What's is the V5 colunmn of GWAS summary statistics in your vignette

[aina91]

Hi, I am interetsed in your work. Excuse me, what does the fifth column of GWAS summary statistics files in vigente represent？
It shows below.

V1 V2 V3 V4 V5

1 chr1 25653526 25653527 region1 1.0000

2 chr1 24850597 24850598 region1 0.0242

3 chr1 24722451 24722452 region1 0.0103

4 chr1 24665802 24665803 region1 0.0096

5 chr1 24994340 24994341 region1 0.0096

6 chr1 25095653 25095654 region1 0.0061

And I also want to known how to make this format GWAS summary statistics files. Is there a script shipped with gchromVAR that does this, or do I just make it by my self?Thanks!

[julirsch]

This is the posterior inclusion probability from fine-mapping. Unfortunately you have to perform fine-mapping yourself.

[aina91]

Yeah,I see. Is there any partial scripts in github which are correlated to 'Genome-wide association studies','Linkage disequilibrium score regression', to get input files ( master files, z files and ld files) of Fine_mapping. It will be very helpful for me to understand and use 'g-chromVAR'. At 2020-09-04 23:34:11, "Jacob Ulirsch" <notifications@github.com> wrote: This is the posterior inclusion probability from fine-mapping. Unfortunately you have to perform fine-mapping yourself. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[julirsch]

I don't think so. There is a nice and clear wiki for how to use LDSC here:
https://github.com/bulik/ldsc/wiki

We essentially just used Unix commands to munge output from BOLT-LMM and FINEMAP, both of which are well documented below:
https://storage.googleapis.com/broad-alkesgroup-public/BOLT-LMM/BOLT-LMM_manual.html
http://www.christianbenner.com