Table 1.

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

Tools	DL model	Application	Input/Output	Website Code Source	References
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]