Off topic:Convert imputed genotypes from IMPUTE2 dosage .gen/.info to vcf format

Question

[1888]

Hi,

Is there an easy way to convert imputed genotypes from probability format like this:

--- rs190467660 10010504 A C 0.929 0.070 0 0.895 0.102 0.002 0.871 
--- rs193112405 10010957 T A 0.973 0.026 0 0.954 0.045 0

• I think this is the output from IMPUTE2 (https://mathgen.stats.ox.ac.uk/impute/impute_v2.html), with 3 values for each SNP and an info file, I do not have a sample file... The info file looks like this:

  snp_id rs_id position exp_freq_a1 info certainty type info_type0 concord_type0 r2_type0 --- rs190467660 10010504 0.070 0.092 0.872 0 -1 -1 -1 --- rs193112405 10010957 0.035 0.112 0.936 0 -1 -1 -1

to VCF format like this?

##fileformat=VCFv4.1
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT UNR1 UNR2    UNR3    UNR4
chr7    123 SNP1    A   G   100 PASS    INFO    GT:DS   0/0:0.001   0/0:0.000   0/1:0.999   1/1:1.999
chr7    456 SNP2    T   C   100 PASS    INFO    GT:DS   0/0:0.001   0/0:0.000   0/1:1.100   0/0:0.100

I am asking because I would like to apply FastQTL (http://fastqtl.sourceforge.net/), but I only have data in the mldose format.

Thank you very much for your help!