Table 1 Genomic tools/algorithm based on deep learning architecture for variant calling and annotations

Clairvoyante

CNN

To predict variant type, zygosity, alternative allele and Indel length

BAM/VCF

https://github.com/aquaskyline/Clairvoyante

[145]

DeepVariant

CNN

To call genetic variants from next-generation DNA sequencing data

BAM,CRAM/VCF

https://github.com/google/deepvariant

[30]

GARFIELD-NGS

DNN + MLP

To classify true and false variants from WES data

VCF/VCF

https://github.com/gedoardo83/GARFIELD-NGS

[146]

Intelli-NGS

ANN

To define good and bad variant calls from Ion Torrent sequencer data

VCF/xlsx

https://github.com/aditya-88/intelli-ngs

[147]

DAVI (Deep Alignment and Variant Identification)

CNN + RNN

To identify variants in NGS reads

FASTQ/VCF

N/A

[116]

DeepSV

CNN

To call genomic deletions by visualising sequence reads

BAM/VCF

https://github.com/CSuperlei/DeepSV

[52]