I am using shapeit v4 to phase my germline mutation calls which I got using GATKs HaplotypeCaller (WGS data). As a reference, I am using the 1000k genome project. I think that everything works well, since the program runs without an error and my samples are phased afterwards, but the issue is that the resulting phased vcf file loses almost all INFO FORMAT and QUAL entries. E.g. for the format, only GT remains. So my question is, if you know whether it is possible to simply "add" the phased Genotypes and keep all other entries of my VCF.
Furthermore, I noticed, that shapeit v4 only retains variants that are shared between the input (my vcf file) and the reference (the 1000k genomes reference vcf file). Do you now if there is an option to keep all variants, and simply ignore the ones that are missing in the reference while phasing?
Any help is much appreciated!