When running a multi-sample analysis in VarSome Clinical, we use joint calling for variants. The variant caller will perform a local realignment of all of the samples' reads around the target region being investigated and then will try to identify the haplotypes supported by the resulting pileup. This way the caller uses the information of all samples to boost the evidence of each variant site.
Use an existing analysis for joint calling
When selecting the option "use an existing analysis", if all of the component analyses were initially launched from FASTQ, joint calling is performed as if re-using the FASTQ files from scratch. The only case where joint calling cannot be implemented is if any of the component analyses were launched starting from a VCF file, for which we only merge the VCF results.