vcf to bgen conversion using qctool v2 yields 0 snps

Question

[kpatil]

Hi all,

I have a vcf file that was extracted from UKB data using qctool (v2.0.6-Ubuntu16.04-x86_64) and contains data in the GP format. This contains a bunch of SNPs from a single chromosome.

❱ wc -l chromosome1.vcf
260 chromosome1.vcf

Then I try to convert this file to .bgen again using qctool but get "0 snps" and the output file is empty.

What am I doing wrong?

qctool -g chromosome1.vcf -vcf-genotype-field GP -og chromosome1.bgen -ofiletype bgen_v1.2 -bgen-bits 8


> Welcome to qctool (version: 2.0.6, revision 18b8f17)
> 
> (C) 2009-2017 University of Oxford
> 
> Opening genotype files                                      :
> [******************************] (1/1,1.3s,0.8/s)
> ========================================================================
> 
> Input SAMPLE file(s):         Output SAMPLE file:             "(n/a)".
> Sample exclusion output file:   "(n/a)".
> 
> Input GEN file(s):
>                                                     (not computed)  "chromosome1.vcf"
>                                          (total 1 sources, number of snps not computed).
>                       Number of samples: 487409 Output GEN file(s):             "chromosome1.bgen" Output SNP position file(s):    (n/a) Sample
> filter:                  .
> # of samples in input files:    487409.
> # of samples after filtering:   487409 (0 filtered out).
> 
> ========================================================================
> 
> filetype hint = "bgen_v1.2", guess is "bgen_v1.2". Processing SNPs    
> :  (0/?,0.3s,0.0/s)
> ========================================================================
> 
> Number of SNPs:
>                      -- in input file(s):                 (not computed).  -- in output file(s):                0
> 
> Number of samples in input file(s):   487409.
> 
> Output GEN files:                     (0      snps) 
> "chromosome1.bgen"
>                                       (total 0 snps).
> ========================================================================
> 
> !! Error (genfile::MalformedInputError): Source "chromosome1.vcf" is malformed on line 4..

The error that the vcf file is malformed on line 4 is quite unexpected for me as this file was also created by qctool and was not touched.

Here is a snippet from the vcf file with the malformed line at the end which is the first line with SNP data:

❱ head -n4 chromosome1.vcf | cut -f1-15
##fileformat=VCFv4.2
##FORMAT=<ID=GP,Type=Float,Number=G,Description="Genotype call probabilities">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  4303212 3351913 2982758 3576795 4579377 5488446
01      2077409 rs385039,1:2077409_A_G  A       G       .       .       .       GP      1,0,0   1,0,0   0,0,1   1,0,0   1,0,0   0,1,0