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Table 3 Comparisons of tools for genome build and allele definition conversions

From: GACT: a Genome build and Allele definition Conversion Tool for SNP imputation and meta-analysis in genetic association studies

Complementary functionality GenGen GWAMA METAL PLINK GACT
Allele definition prediction No No No No Yes
Uninformed strand/allele flip1 No Yes Yes Yes No
Informed allele conversion2 Yes3 No No No Yes
Automatic allele conversion Yes3 No No No4 Yes
Genome build prediction No No No No Yes
Genome build conversion No No No Yes4 Yes
Command line Yes Yes Yes Yes Yes
Interactive web interface No No No No Yes
  1. 1“Uninformed” refers to flipping without SNP allele annotation knowledge.
  2. 2“Informed” refers to use of the original SNP definition and microarray-specific annotation information.
  3. 3GenGen converts between Top, Forward, A/B and 1/2 allele definitions; by comparison, GACT converts between Top, Forward, A/B and Plus definitions while the Plus definition is used by the 1000 Genomes Project and most next-generation sequencing studies.
  4. 4PLINK can strand- or allele-flip but it cannot directly convert from one allele definition to another, unless the user manually extracts information from the microarray annotation file; by comparison, GACT automatically converts between genome builds and allele definitions.