Twelve years of SAMtools and BCFtools

HTSlib: C library for reading/writing high-throughput sequencing data

(2021) James K Bonfield et al.   GigaScience

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Comparison of Read Mapping and Variant Calling Tools for the Analysis of Plant NGS Data

(2020) Hanna Marie Schilbert et al.   Plants-Basel

Crumble: reference free lossy compression of sequence quality values

(2018) James K Bonfield et al.   BIOINFORMATICS

Bioconda: sustainable and comprehensive software distribution for the life sciences

(2018) Björn Grüning et al.   NATURE METHODS

BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data

(2016) Vagheesh Narasimhan et al.   BIOINFORMATICS

A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data

(2016) Petr Danecek et al.   PLoS One

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Improving SNP discovery by base alignment quality

(2011) H. Li   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Efficient storage of high throughput DNA sequencing data using reference-based compression

(2011) M. Hsi-Yang Fritz et al.   GENOME RESEARCH

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS