huwenboshi / impg Goto Github PK

ImpG outputs Z-score and Var of many imputed SNPs. I would further need beta (or alternatively ln(OR)), and the associated standard error. Is it possible?

the line:
"if(indv not in added):"
from:
ImpG/ImpG-Utils/ExtractPop
refers to the variable "added", which isnt defined anywhere else in the code.

Hello. I ran ImpG and I compared these results with imputed data from impute2, getting a Pearson correlation score of 0.93. I think it's ok, but would it be possible to have sample input and sample output data (maybe of a small chromosome) so that I can check that I'm doing everything right? Please let me know. Thanks

I have about 30 different GWAS results with z-scores and I'm trying to apply ImpG to each of studies. I noticed that I can use the same haps/ and maps/ for all these traits. My workflow is done 4.2.1, 4.2.2, 4.2.3 once and repeat 4.2.4.2, 4.2.5, 4.2.6 and 4.2.7 for 30 different GWAS results.
I noticed that it takes more than 3 days for step 4.2.5 to complete for the larger chromosomes. I'm wondering if I can use the same beta file for all the GWAS results. In other words, can I complete step 4.2.5 one time and use the same beta output for rest of the GWAS results? By the way, what is the output of the GenBeta command? It looks like a SNPxSNP matrix, but I'm not sure what the values are.

Hi,

Recently i want to do some researches about the imputation using summary results, and the offical download website of imgG doesn't works (i can't open it), so i am trying to install it from Github, but i find there is nothing described about the installation of impG, could you please give me some suggestions for it?

Thanks in advance

Lilin

Hi there,
I want to impute my summary data of WTCCC1 to 1000Genome, i find the SNPs that share the same names in those tow datasets have different physical position. For example:
In WTCCC1:
1 rs4040617 0 819185 G A
In 1000Genome:
1 rs4040617 0 779322 G A
I don't know why this happened. They are treated as different SNPs when running ImpG, could i just directly replace one of them by another?
Thanks in advance.

Hi there,

When I ran ImpG sample data set, I got all '0' in the z-score column of imputed file, is this expected? Besides, what does 'r2pred' mean?

   1 SNP_name SNP_pos Ref_Allele Alt_Allele Z-Score r2pred
   2 rs58108140 10583 G A 0.000000 0.047726
   3 rs189107123 10611 C G 0.000000 0.168957
   4 rs180734498 13302 C T 0.000000 0.072032
   5 rs144762171 13327 G C 0.000000 0.125312
   6 rs151276478 13980 T C 0.000000 0.147011
   7 rs140337953 30923 G T 0.000000 0.070191
   8 rs187298206 51476 T C 0.000000 0.000000
   9 rs116400033 51479 T A 0.000000 0.034429
  10 rs62637813 52058 G C 0.000000 0.022032
  11 rs190291950 52144 T A 0.000000 0.084958
  12 rs150021059 52238 T G 0.000000 0.047977

Thanks.

Hello!
I have noticed that while running ImpG there might be problems when alleles in my input Z-score file (ZF) differ from the provided mapping file (MF). Am I right?
Basically, I have four cases:
1 - Alt allele and Ref allele match in my ZF and in the MF;
2 - Alt allele and Ref allele are inverted in my ZF with respect to the MF (e.g.: Alt allele in MF = A; Ref allele in MF = G; Alt allele in ZF = G; Ref allele in ZF = A);
3 - Alt allele and Ref allele in my ZF are the complement of Alt allele and Ref allele in the MF (e.g.: Alt allele in MF = A; Ref allele in MF = G; Alt allele in ZF = T; Ref allele in ZF = C);
4 - Alt allele and Ref allele in my ZF are inverted and the complement of Alt allele and Ref allele in the MF (e.g.: Alt allele in MF = A; Ref allele in MF = G; Alt allele in ZF = C; Ref allele in ZF = T);

If I understand correctly, I can still use ImpG, provided that I make the alleles in my ZF consistent with the alleles in the MF. When flipping or inverting, however, I also should invert z-scores in some cases (case 2 and 4): am I right?

Please, let me know. Thanks, best regards