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This repository has been archived by the owner on Feb 28, 2023. It is now read-only.
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.
The text was updated successfully, but these errors were encountered:
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.
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
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.
The text was updated successfully, but these errors were encountered: