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

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!

snp vcf

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updated 10.0 years ago by annonymous3683 •

• written 10.4 years ago by 1888

where can we get a description of this mldose format ?

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written 10.4 years ago by Pierre Lindenbaum

I am sorry, I think if I have the format right as IMPUTE2, then this answer (How to convert IMPUTE2 to VCF format) advises to use QCtool, command:qctool -g data.gen -og example.vcf (http://www.well.ox.ac.uk/~gav/qctool/#tutorial), which produces this output:

##fileformat=VCFv4.1
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype calls">
##FORMAT=<ID=GP,Number=3,Type=Float,Description="Genotype call probabilities">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  sample_1        sample_2
NA      10010504        rs190467660     A       C       .       .       .       GT:GP   0/0:0.929,0.07,0        ./.:0.895,0.102,0.002   ./.:0.871
NA      10010957        rs193112405     T       A       .       .       .       GT:GP   0/0:0.973,0.026,0       0/0:0.954,0.045,0       0/0:0.94,0.06

But this is not correct as I think it assumes genotyped values and not dosages (GT:GP while I am looking for the GT:DS and one value per sample)... Is there another tool to help convert these formats? I see there could be another option using fcgene (https://sourceforge.net/p/fcgene/wiki/Genotype%20format%20converting%20tool%20:%20FCgene/), maybe converting from IMPUTE2 -> Plink -> VCF. Is there a more direct way?

Thank you

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written 10.4 years ago by 1888

Were you able to resolve this problem? I also need to convert IMPUTE2 .gprobs files to .vcf format and qctools is only able to process a few lines of data with unclear exit.

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written 10.0 years ago by annonymous3683 •

Hello 1888!

Questions similar to yours can already be found at:

How to convert IMPUTE2 to VCF format

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

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written 6.7 years ago by zx8754

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