Many workflows use more than one variant caller for the same sample and create a consensus from these.
For example, for sample A the three variant callers strelka, freebayes and mutect2 could be used and a filter criteria might be the number of variant callers reporting this variants (e.g., at least 2 callers report the variant).
Hence, I suggest the following for this feature:
Based on the samplesheet, this process could identify multiple VCF files with the same sample name and automatically merge those, giving a warning message into the multiQC report.
a configuration parameter in the workflow could disable the automatic merging.
Once multi-sample VCF files are supported (Issue #35) the workflow could preprocess VCF files from the same sample into a multi-sample VCF file. the VCF file name could serve as sample name.
The processing might enforce specific normalization steps prior to merging the VCF files to avoid having the same variant in multiple times in different definitions.
The workflow should add an additional annotation column giving the number of VCF files in which the respective variant occurred. Another column should give the name of these files, enabling specific filtering, e.g., for specific variant caller.
Additional checks might be implemented, e.g., to ensure no variants are dropped during the process.
Description of feature
Many workflows use more than one variant caller for the same sample and create a consensus from these. For example, for sample A the three variant callers strelka, freebayes and mutect2 could be used and a filter criteria might be the number of variant callers reporting this variants (e.g., at least 2 callers report the variant).
Hence, I suggest the following for this feature: