I am doing a GWAS with imputed genotypes (phased with Eagle, imputed with Impute2), that resulted in a format similar to this:
--- rs17149628:126006965:C:T 126006965 C T
After imputation, an analysis using SNPTEST went absolutely fine, without producing errors.
However, I am now trying to extract certain SNP status for all individuals using QCTOOL and it seems there's an issue when I try to specify the rsID (second field, i.e.
rs17149628:126006965:C:T) as no output is produced (however no errors are listed s). My guess is QCTOOL reads ":" as a field separator and isn't able to treat it as a SNP. Would anyone know how to overcome the problem?
The whole log is as follows:
qctool -g data.impute2 -s sample.txt -incl-rsids snp.txt -og extract.txt (C) 2009-2011 University of Oxford Opening genotype files : (1/1,0.0s,33.6/s) =================================================================== Input SAMPLE file(s): "sample.txt" Output SAMPLE file: "(n/a)". Sample statistic output file: "(n/a)". Sample exclusion output file: "(n/a)". Input GEN file(s): (not computed) "snp-id-data-filtered:data.impute2" (total 1 sources, number of snps not computed). Number of samples: 653 Output GEN file(s): "extract.txt" Output SNP position file(s): (n/a) SNP statistic output file(s): Sample filter: (none). SNP filter: (none). # of samples in input files: 653. # of samples after filtering: 653 (0 filtered out). =============================================================== Processing SNPs : (1/?,21.2s,0.0/s) =============================================================== Number of SNPs: -- in input file(s): (not computed). -- in output file(s): 1 Number of samples in input file(s): 653. Output GEN files: (1 snps) "extract.txt" (total 1 snps). ======================================================================== Thank you for using qctool.
So, all seems fine, but the
extract.txt is empty. I am becoming desperate here, would anyone know what/why is happening and how to overcome it? I'll be thankful for any comments!