I am trying to convert .gen file to .bgen format. Unfortunately, I am facing an error while doing it. Below find my command line and the error that I am facing:
~/SIGN/packages/qctool_v1.0-static-linux-x86-64 -g stroke.group4.consensus.EUR.QC2.chr13.imputed -og example.bgen -force
Welcome to qctool, version 1.4 (C) 2009-2012 University of Oxford
(Constructing SNP filter...) (0.0s) (Constructing sample filter...) (0.0s) (Opening gen file "./stroke.group4.consensus.EUR.QC2.chr13.imputed"...)Constructing chromosome from "". (1219.6s) Opened 1 GEN files in 1219.6s. ========================================================================
Input SAMPLE file: "(n/a)". Output SAMPLE file: "(n/a)".
Sample statistic output file: "(n/a)". Sample exclusion output file: "(n/a)".
Input GEN file(s): (1644669 snps) "./stroke.group4.consensus.EUR.QC2.chr13.imputed" (total 1644669 snps in input). Output GEN file(s): "example.bgen"
Output SNP position file(s): (n/a) SNP statistic output file(s): Sample filter: (none). SNP filter: (none).
# of samples in input files: 15779. # of samples after filtering: 15779 (0 filtered out).
!! WARNING: You have specified output GEN (or snp exclusion) files, but no filters. This will just output the same gen files (converting formats if necessary). Consider using gen-convert, included with the qctool source code, instead.
!! Warnings were encountered, but proceeding anyway as -force was supplied.
Processing SNPs... [ ] (55 / 1644669, 1220.6s)qctool_v1.0-static-linux-x86-64: genfile/src/GenFileSNPDataSource.cpp:67: virtual void genfile::GenFileSNPDataSource::read_snp_probability_data_impl(const boost::function<void(size_t, double, double, double)>&): Assertion `this_data_number_of_samples == number_of_samples()' failed. Aborted
Can someone please help me to resolve the issue?
Also, can someone please help me to design a command line for extraction of data for specific list of SNPs?