Replace REF and ALT columns based on the GT of one sample in a VCF file

Question

[charlesberkn]

Hi,

I have a VCF file with three samples that looks something like this:

#CHROM POS     ID        REF    ALT     QUAL FILTER INFO                              FORMAT      NA00001        NA00002        NA00003
20     14370   rs6054257 G      A       29   PASS   NS=3;DP=14;AF=0.5;DB;H2           GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
20     17330   .         T      A       3    q10    NS=3;DP=11;AF=0.017               GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3   0/0:41:3
20     1110696 rs6040355 A      G,T     67   PASS   NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2   2/2:35:4

I want to replace REF and ALT columns based on the genotype (GT) of one sample. For example, I replace REF and ALT columns based on the GT of the third

sample (NA00003), and, after replacing, I have:

#CHROM POS     ID        REF    ALT     QUAL FILTER INFO                              FORMAT      NA00001        NA00002        NA00003
20     14370   rs6054257 A      A       29   PASS   NS=3;DP=14;AF=0.5;DB;H2           GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
20     17330   .         T      T       3    q10    NS=3;DP=11;AF=0.017               GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3   0/0:41:3
20     1110696 rs6040355 T      T       67   PASS   NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2   2/2:35:4

Can anybody help me get this done? Thank you.

[Pierre Lindenbaum]

why would you want to do that ?

[charlesberkn]

We are developing a statistical model to infer the true genotypes based on several samples.

[Jorge Amigo]

then you'll have to play around with the genotype information, and not with the variant definition. if you change the REF and ALT information then all the samples' genotype information won't make any sense, at least in the VCF format context.