rgcgithub/regenie

Fraction of genes have no gene_p results

Mathias0077 opened this issue · 3 comments

Mathias0077 commented

Hi Joelle,

I hope you're well. I'd be grateful if you could please help me with a problem in gene based burden testing using the --rgc-gene-p command.

The output to the console reports no issue or problem during the run but in the results file we find the gene_p statistics only for a fraction (~60%) of all genes. I paste you an example output of results (i, gene SPTLC1) with gene_p and (ii, gene SUSD3) without gene_p results.
While there is no output of a problem on insufficient data/ rare allele counts or similar, I wonder, what happened and if there might a way to get information about the problem to potentially solve it and to have the gene_p test for all genes? By the way, we cannot observe a pattern, that for example, only for genes with a low number of rare variants the gene_p is not in the results file - this also happens for genes with a higher number of rare variants compared to other genes with a lower number of rare variants and gene_p in the results. And we do the analyses for all autosomal genes for a balanced (1:1) cases/ control outcome.

Any help is highly appreciated.

Thank you, best Mathias

grafik

joellembatchou commented
Mathias0077 commented

Hi Joelle,

thank you for looking into this. The summary stats are those posted in my initial message. I added the logfile to this thread. There are 94 and 35 variants in the genes and the exepected information is provided for both genes:

 -reading in genotypes, computing gene-based tests and building masks...done (xxx ms) 
 -computing association tests...done (xx ms) 
 -computing joint association tests...done (x ms)

the logfiles do not report an error this. I hope this information is helpful.

Best,
Mathias

tocheck.log

joellembatchou commented

Hi,

Can you re-run just for gene "SUSD3" including the option --debug? Please send both the output from stdout & stderr.