Twelve years of SAMtools and BCFtools

Danecek, Petr; Bonfield, James K.; Liddle, Jennifer; Marshall, John; Ohan, Valeriu; Pollard, Martin; Whitwham, Andrew; Keane, Thomas M.; McCarthy, Shane; Davies, Robert M.; Li, Heng

doi:10.1093/gigascience/giab008

Cited by 7,699 publications

(5,961 citation statements)

References 22 publications

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“…The alignment files that were generated for each reference sequence were used for the detection of SNP positions using MPileup v2.1.1 [34,35]. Variant sites only were kept by using BCFTools v1.0 [36], resulting in 1723 and 1785 variable SNP positions for the BmNPV-My and BmNPV-India reference-based analysis, respectively. Variable SNP positions were analyzed quantitatively and qualitatively by using the bacsnp v0.1.4 package in R (R v4.0.3 in RStudio v1.1.443) [37].…”

Section: Snp Genotyping Of Bmnpv and Bmbdv Isolatesmentioning

confidence: 99%

Patterns in Genotype Composition of Indian Isolates of the Bombyx mori Nucleopolyhedrovirus and Bombyx mori Bidensovirus

Gani

Senger

Lokanath

et al. 2021

Viruses

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The mulberry silkworm, Bombyx mori (L.), is a model organism of lepidopteran insects with high economic importance. The viral diseases of the silkworm caused by Bombyx mori nucleopolyhedrovirus (BmNPV) and Bombyx mori bidensovirus (BmBDV) inflict huge economic losses and significantly impact the sericulture industry of India and other countries. To understand the distribution of Indian isolates of the BmNPV and to investigate their genetic composition, an in-depth population structure analysis was conducted using comprehensive and newly developed genomic analysis methods. The seven new Indian BmNPV isolates from Anantapur, Dehradun, Ghumarwin, Jammu, Kashmir, Mysore and Salem grouped in the BmNPV clade, and are most closely related to Autographa californica multiple nucleopolyhedrovirus and Rachiplusia ou multiple nucleopolyhedrovirus on the basis of gene sequencing and phylogenetic analyses of the partial polh, lef-8 and lef-9 gene fragments. The whole genome sequencing of three Indian BmNPV isolates from Mysore (-My), Jammu (-Ja) and Dehradun (-De) was conducted, and intra-isolate genetic variability was analyzed on the basis of variable SNP positions and the frequencies of alternative nucleotides. The results revealed that the BmNPV-De and BmNPV-Ja isolates are highly similar in their genotypic composition, whereas the population structure of BmNPV-My appeared rather pure and homogenous, with almost no or few genetic variations. The BmNPV-De and BmNPV-Ja samples further contained a significant amount of BmBDV belonging to the Bidnaviridae family. We elucidated the genotype composition within Indian BmNPV and BmBDV isolates, and the results presented have broad implications for our understanding of the genetic diversity and evolution of BmNPV and co-occurring BmBDV isolates.

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Section: Snp Genotyping Of Bmnpv and Bmbdv Isolatesmentioning

confidence: 99%

Patterns in Genotype Composition of Indian Isolates of the Bombyx mori Nucleopolyhedrovirus and Bombyx mori Bidensovirus

Gani

Senger

Lokanath

et al. 2021

Viruses

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“…A wide range of solutions exist for VCF processing that make use of these three approaches and functional overlap is found between vcflib, bio-vcf, cyvcf2, the original vcftools [2], bcftools [7] and the existing Bio* programming libraries, such as biopython [25], bioruby [27] and biojava [41]. vcftools and bcftools provide annotation, merging, normalization and filtering capabilities that complement functionality and can be combined in workflows with vcflib and bio-vcf.…”

Section: Software Development and Distribution Practicesmentioning

confidence: 99%

Vcflib and tools for processing the VCF variant call format

Garrison

Kronenberg

Dawson

et al. 2021

Preprint

104

101

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Since its introduction in 2011 the variant call format (VCF) has been widely adopted for processing DNA and RNA variants in practically all population studies --- as well as in somatic and germline mutation studies. VCF can present single nucleotide variants, multi-nucleotide variants, insertions and deletions, and simple structural variants called against a reference genome. Here we present over 125 useful and much used free and open source software tools and libraries, part of vcflib tools and bio-vcf. We also highlight cyvcf2, hts-nim and slivar tools. Application is typically in the comparison, filtering, normalisation, smoothing, annotation, statistics, visualisation and exporting of variants. Our tools run daily and invisibly in pipelines and countless shell scripts. Our tools are part of a wider bioinformatics ecosystem and we consider it very important to make these tools available as free and open source software to all bioinformaticians so they can be deployed through software distributions, such as Debian, GNU Guix and Bioconda. vcflib, for example, was installed over 40,000 times and bio-vcf was installed over 15,000 times through Bioconda by December 2020. We shortly discuss the design of VCF, lessons learnt, and how we can address more complex variation that can not easily be represented by the VCF format. All source code is published under free and open source software licenses and can be downloaded and installed from https://github.com/vcflib.

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“…Read coverage of the reference genome was calculated using samtools mpileup with the default settings plus `-aa -C 50 -q 10 -Q 10` to output all positions, adjust mapping quality using mismatches and exclude reads with a minimum mapping quality < 10 and positions with a base quality < 10. Variants were identified using bcftools v1.9 (Danecek et al, 2021) mpileup with the same settings. Variants were filtered and quantified using the Python packages pyvcf (v0.6.8) (Casbon, 2012) and pysam (v0.15.4) (Heger and Jacobs, 2009).…”

Section: Virus Sequencingmentioning

confidence: 99%

pUL21 is a viral phosphatase adaptor that promotes herpes simplex virus replication and spread

Benedyk

Muenzner

Connor

et al. 2021

Preprint

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The herpes simplex virus (HSV)-1 protein pUL21 is essential for efficient virus replication and dissemination. While pUL21 has been shown to promote multiple steps of virus assembly and spread, the molecular basis of its function remained unclear. Here we identify that pUL21 is a virus-encoded adaptor of protein phosphatase 1 (PP1). pUL21 directs the dephosphorylation of cellular and virus proteins, including components of the viral nuclear egress complex, and we define a conserved non-canonical linear motif in pUL21 that is essential for PP1 recruitment. In vitro evolution experiments reveal that pUL21 directly antagonises the activity of the virus-encoded kinase pUS3, with growth and spread of pUL21 PP1-binding mutant viruses being restored when pUS3 activity is disrupted. This study shows that virus-directed phosphatase activity is essential for efficient herpesvirus assembly and spread, highlighting the fine balance between kinase and phosphatase activity required for optimal virus replication.

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Twelve years of SAMtools and BCFtools

Cited by 7,699 publications

References 22 publications

Patterns in Genotype Composition of Indian Isolates of the Bombyx mori Nucleopolyhedrovirus and Bombyx mori Bidensovirus

Patterns in Genotype Composition of Indian Isolates of the Bombyx mori Nucleopolyhedrovirus and Bombyx mori Bidensovirus

Vcflib and tools for processing the VCF variant call format

pUL21 is a viral phosphatase adaptor that promotes herpes simplex virus replication and spread

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