| Model/Command | Time (real) | Peak RAM | Output size (VCF) | | :--- | :--- | :--- | :--- | | samtools view -h in.bam chr1 (extract) | 12s | 1.2GB | 4.5GB (SAM) | | Model B: samtools sort -@8 (8 threads) | 14m 22s | 6.8GB | 95GB (BAM) | | Model C: samtools mpileup -uf ref.fa in.bam | bcftools call -mv | 48m 31s | 2.1GB | 2.3MB (VCF) | | Model D: GATK HaplotypeCaller (for comparison) | 3h 12m | 8.7GB | 3.1MB (VCF) |
SAMTool releases updates every 2–3 months. As of Q2 2025, version 2.8.9 has added preliminary support for: samtool supported models
In the context of variant calling, "models" often refers to the mathematical modeling of variants (SNPs vs. Indels). SAMtools implements these models via bcftools (the variant calling companion tool). | Model/Command | Time (real) | Peak RAM
: Includes models of varying complexity, from simple production models to data-rich integrated assessments. SAMtools implements these models via bcftools (the variant