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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:

example of horizontal merge

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:

example of vertical merge

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Tool for merging large sets of VCF files

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