EVA VCF Merge
Library to merge VCF files horizontally and vertically.
Dependencies
Besides the dependencies in requirements.txt, the module also uses Nextflow to manage
merging large numbers of files, which itself requires Java 8. See Nextflow documentation for details on installation.
Horizontal Merge
Horizontally mergeable VCFs have non-overlapping sample sets and can be combined to create a single multi-sample
file, using e.g. bcftools merge.
For example, if one VCF file has samples S1, S2, S3 while the second has S4, they can be horizontally
merged and the resulting file will have samples S1, S2, S3, S4:
Vertical Merge
Vertically mergeable VCFs have identical sample sets and can be combined to create a single multi-chromosome or
multi-variant file, using e.g. bcftools concat.
For example, if two VCF files both have samples S1, S2, S3 with different variants, they can be vertically merged:
