Combine multiple VCF files

Since HaploGrep2 currently accepts the upload of a single file only, the upload of single VCF files can be cumbersome. As a workaround you can merge single VCF files into one large VCF file. In order to do so there are several ways:

a) GATKs – CombineVariants
b) VCFlib – vcfcombine
c) VCFtools – vcf-merge
Example usage (Samtools tabix required)

Hope this helps!

Hansi has written 14 articles

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