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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.