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Yves-CHEN / DENTIST

DENTIST (Detecting Errors iN analyses of summary staTISTics) is a QC tool for summary-data-based analyses.
GNU Lesser General Public License v3.0
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[error] No. of interval is 0 #24

Open ulkerjanan opened 8 months ago

ulkerjanan commented 8 months ago

Hello , I am using DENTIST 1.3 and using GWAS summary statistics data downloaded from PGC and UK Biobank imputed genotypes file as input. This is what i have in my log file which seems strange to me:

GWAS summary data of 6035928 SNPs to be included from ..... [warning] mogan is like to be missing, but it will only be a problem when calling for it. [info] Calculating frequencies with 1 cpus [info] chrID == 3 [info] Aligning GWAS to the reference sample assumming both files are ordered. [info] Performing DENTIST at 48 SNPs shared between the summary and reference data. No. of gaps found: 45

First of all, only 48 SNPs shared between the summary and reference data is too little as I have very big files. Then I get this error at the end of each chr processing : [error] No. of interval is 0

Could you please tell me what could be the problem here? I am using a for loop for chromosomes because i have one common file for imputed genotypes. Thanks in advance!

Yves-CHEN commented 8 months ago

Thanks very much for your interest, Ulker.

First of all, only 48 SNPs shared between the summary and reference data is too little as I have very big files. Then I get this error at the end of each chr processing : [error] No. of interval is 0 Could you please tell me what could be the problem here? I am using a for loop for chromosomes because i have one common file for imputed genotypes. Thanks in advance!”

The 48 SNPs is indeed strange. The way DENTIST to identify the shared SNPs between summary and LD reference data is by creating ID as chr-start-A1-A2, A1 and A2 are sorted, so that the ordering does not matter. I suppose you can then check this accordingly.