scDeepVariant Model Checkpoints

Available Models

Base Models (6-channel)

• base_6_ckpt/ - Base model with checkpointing
• base_6_nockpt/ - Base model without checkpointing

Allele Frequency Models (scDV-AF)

• 1kgp/ - Model trained with 1000 Genomes Project allele frequencies
• gnomad/ - Model trained with gnomAD allele frequencies
• gnomad_pass/ - Model trained with filtered gnomAD (PASS variants only)

Usage

• For standard variant calling without population information: use base_6_* models
• For variant calling with allele frequency information: use one of the AF models (1kgp/, gnomad/, or gnomad_pass/)