Original samtools variant calling (bcftools call -c)

Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics (2011) 27(21) 2987-93. link

BAQ calculation

Li H. Improving SNP discovery by base alignment quality. Bioinformatics (2011) 27(8):1157-8. link

Detecting runs of homozygozity (bcftools roh)

Narasimhan V, Danecek P, Scally A, Xue Y, Tyler-Smith C, and Durbin R. BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data. Bioinformatics (2016) 32(11) 1749-51 link

CNV calling (bcftools cnv and bcftools polysomy)

Danecek P, McCarthy SA, HipSci Consortium, and Durbin R. A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data, PLoS One (2016) 11(5) e0155014 link

Consequence calling (bcftools csq)

Danecek P, McCarthy SA. BCFtools/csq: Haplotype-aware variant consequences. Bioinformatics (2017) 33(13) 2037-39 link

All of BCFtools, file manipuplation, -m calling, etc

Danecek P, Bonfield JK, et al. Twelve years of SAMtools and BCFtools. Gigascience (2021) 10(2):giab008 link

Various math notes

  • Multiallelic calling (bcftools call -m) pdf

  • BCFtools/trio-dnm calling (bcftools +trio-dnm2) pdf

  • SAMtools math notes pdf

  • SegBias calculation pdf


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