Different number of variants in summary statistics file and postgap results

[11Dmitriy11]

I found that postgap --summary_stats skips some variants from summary statistics file (variants that are parsed with --rsID and passes the threshold) and there are defferent number of variants in postgap result file and summary statiscits file. Is there a way to change the parameters so that result file contains all rsids (that can be successfully parsed) from summary statistics file.

[dzerbino]

Hello @11Dmitriy11 ,

There are indeed quite a few steps where SNPs are dropped, typically if they do not show up in the 1000 genomes genotypes. If you are willing to share with me the rsID of a SNP that was dropped, I can have a look at understanding why they dissappeared.

Regards,

Daniel

[11Dmitriy11]

Hello @dzerbino,
Here is list of rsids from summary file that a not present in gwas_snp and ld_snp_rsID columns, correspondingly. Also there are input summary file for postgap (UKBB phenotype 'never smoked'). P value threshold for postgap was 1e-4.
20116_0.gwas.imputed_v3.both_sexes_chr8_FILTERED.txt
gwas_snp.txt
ld_snp_rsID.txt
I am interested in rs4246125 from intron region of PTK2 gene

[11Dmitriy11]

Hello @dzerbino,
Are there any updates?

[dzerbino]

Hello @11Dmitriy11 ,

No sorry, I've been snowed under the past few weeks, I'll try this weekend.

Regards,

Daniel