Is it possible to combine single sample VCF files to multi sample VCF files? The samples are different strains from the same species, mapped against the same reference.
The single sample vcf files have been made with GATK and the multi sample vcf file should preferentially also be compatible with GATK for downstream processing.
We chose not to do multi-sample calling in GATK because we don't want the genotype calls and their quality from one sample to be influenced by the genotype calls and their quality from other samples (which GATK does by default when doing multi-sample calling ).
We do however want to to process the samples the and their genotypes as one big matrix.