Closed:Extracting SNP status using QCTOOL from an impute2 output

Question

[Mardze]

Hi everyone!

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! Nad