The variant call format and VCFtools

Danecek, Petr; Auton, Adam; Abecasis, Gonçalo R.; Albers, Cornelis A.; Banks, Eric; DePristo, Mark A.; Handsaker, Robert E.; Lunter, Gerton; Marth, Gábor; Sherry, Stephen T.; McVean, Gil; Durbin, Richard

doi:10.1093/bioinformatics/btr330

Cited by 12,609 publications

(11,396 citation statements)

References 4 publications

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“…By excluding the ones located on unanchored scaffolds, we reduced the number of variants to 13,286,870. We used VCFtools v0.1.14 (Danecek et al., 2011) for the filtering process with the following parameters: minimum read depth (min_DP): 3; maximum read depth (max_DP): 5000; and minimum Phred‐scaled quality score (min_QUAL): 20. We used the R package VcfR (Knaus and Grünwald, 2017) to visualize the distribution of the quality parameters.…”

Section: Methodsmentioning

confidence: 99%

Capturing variation in Lens (Fabaceae): Development and utility of an exome capture array for lentil

et al. 2018

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Premise of the StudyLentil is an important legume crop with reduced genetic diversity caused by domestication bottlenecks. Due to its large and complex genome, tools for reduced representation sequencing are needed. We developed an exome capture array for use in various genetic diversity studies.MethodsBased on the CDC Redberry draft genome, we developed an exome capture array using multiple sources of transcript resources. The probes were designed to target not only the cultivated lentil, but also wild species. We assessed the utility of the developed method by applying the generated data set to population structure and phylogenetic analyses.ResultsThe data set includes 16 wild lentils and 22 cultivar accessions of lentil. Alignment rates were over 90%, and the genic regions were well represented in the capture array. After stringent filtering, 6.5 million high‐quality variants were called, and the data set was used to assess the interspecific relationships within the genus Lens.DiscussionThe developed exome capture array provides large amounts of genomic data to be used in many downstream analyses. The method will have useful applications in marker‐assisted breeding programs aiming to improve the quality of cultivated lentil.

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Section: Methodsmentioning

confidence: 99%

Capturing variation in Lens (Fabaceae): Development and utility of an exome capture array for lentil

et al. 2018

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“…SNP variants were then called using the samtools mpileup command with parameters ‐uD, ‐E, and ‐f (Li et al., 2009). The program vcftools (Danecek et al., 2011) was used to filter for SNPs that exhibited minor allele frequencies of <1% and minimum mean sequencing depths of 50 over all individuals. For downstream analysis, a data matrix was created containing the genotype information for each SNP and individual along with the classifier information on sex, population, sampling year, sea stage (1SW/MSW), and fork length.…”

Section: Methodsmentioning

confidence: 99%

Characterization of natural variation in North American Atlantic Salmon populations (Salmonidae: Salmo salar) at a locus with a major effect on sea age

Kusche

Côté

Hernández

et al. 2017

Ecology and Evolution

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Age at maturity is a key life‐history trait of most organisms. In anadromous salmonid fishes such as Atlantic Salmon (Salmo salar), age at sexual maturity is associated with sea age, the number of years spent at sea before the spawning migration. For the first time, we investigated the presence of two nonsynonymous vgll3 polymorphisms in North American Atlantic Salmon populations that relate to sea age in European salmon and quantified the natural variation at these and two additional candidate SNPs from two other genes. A targeted resequencing assay was developed and 1,505 returning adult individuals of size‐inferred sea age and sex from four populations were genotyped. Across three of four populations sampled in Québec, Canada, the late‐maturing component (MSW) of the population of a given sex exhibited higher proportions of SNP genotypes 54Thrvgll3 and 323Lysvgll3 compared to early‐maturing fish (1SW), for example, 85% versus 53% of females from Trinité River carried 323Lysvgll3 (n MSW = 205 vs. n 1SW = 30; p < .001). However, the association between vgll3 polymorphism and sea age was more pronounced in females than in males in the rivers we studied. Logistic regression analysis of vgll3 SNP genotypes revealed increased probabilities of exhibiting higher sea age for 54Thrvgll3 and 323Lysvgll3 genotypes compared to alternative genotypes, depending on population and sex. Moreover, individuals carrying the heterozygous vgll3 SNP genotypes were more likely (>66%) to be female. In summary, two nonsynonymous vgll3 polymorphisms were confirmed in North American populations of Atlantic Salmon and our results suggest that variation at those loci correlates with sea age and sex. Our results also suggest that this correlation varies among populations. Future work would benefit from a more balanced sampling and from adding data on juvenile riverine life stages to contrast our data.

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“…After retaining only SNPs with the selectvariants module of gatk to avoid later uncertainties in alignments, variants have been further filtered out if any of the following criteria were fulfilled: the quality normalized by the coverage (QD) was <2.0, the Phred‐scaled p ‐value for Fisher's exact test to detect strand bias (FS) was >60.0, or the root mean square of mapping quality across all samples (MQ) was <40. Diversity measures were calculated with vcftools v .0.1.14 (Danecek et al., 2011) with the options –het (for the per‐individual heterozygosity and inbreeding coefficient F ), –site‐pi (for per site nucleotide divergence π) and –singletons (for private alleles).…”

Section: Methodsmentioning

confidence: 99%

Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima

et al. 2017

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The orchid family is the largest in the angiosperms, but little is known about the molecular basis of the significant variation they exhibit. We investigate here the transcriptomic divergence between two European terrestrial orchids, Dactylorhiza incarnata and Dactylorhiza fuchsii, and integrate these results in the context of their distinct ecologies that we also document. Clear signals of lineage‐specific adaptive evolution of protein‐coding sequences are identified, notably targeting elements of biotic defence, including both physical and chemical adaptations in the context of divergent pools of pathogens and herbivores. In turn, a substantial regulatory divergence between the two species appears linked to adaptation/acclimation to abiotic conditions. Several of the pathways affected by differential expression are also targeted by deviating post‐transcriptional regulation via sRNAs. Finally, D. incarnata appears to suffer from insufficient sRNA control over the activity of RNA‐dependent DNA polymerase, resulting in increased activity of class I transposable elements and, over time, in larger genome size than that of D. fuchsii. The extensive molecular divergence between the two species suggests significant genomic and transcriptomic shock in their hybrids and offers insights into the difficulty of coexistence at the homoploid level. Altogether, biological response to selection, accumulated during the history of these orchids, appears governed by their microenvironmental context, in which biotic and abiotic pressures act synergistically to shape transcriptome structure, expression and regulation.

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The variant call format and VCFtools

Cited by 12,609 publications

References 4 publications

Capturing variation in Lens (Fabaceae): Development and utility of an exome capture array for lentil

Capturing variation in Lens (Fabaceae): Development and utility of an exome capture array for lentil

Characterization of natural variation in North American Atlantic Salmon populations (Salmonidae: Salmo salar) at a locus with a major effect on sea age

Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza) with distinct ecological optima

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