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!