Vcflib and tools for processing the VCF variant call format

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.

Genetic mechanisms and correlational selection structure trait variation in a coral snake mimic

Covariation among traits shapes both phenotypic evolution and ecological interactions across space and time. However, rampant geographical variation in the strength and direction of such correlations can be particularly difficult to explain through generalized mechanisms. By integrating population genomics, surveys of natural history collections and spatially explicit analyses, we tested multiple drivers of trait correlations in a coral snake mimic that exhibits remarkable polymorphism in mimetic and non-mimetic colour traits. We found that although such traits co-occur extensively across space, correlations were best explained by a mixture of genetic architecture and correlational selection, rather than by any single mechanism. Our findings suggest that spatially complex trait distributions may be driven more by the simple interaction between multiple processes than by complex variation in one mechanism alone. These interactions are particularly important in mimicry systems, which frequently generate striking geographical variation and genetic correlations among colour pattern traits.

Dental microwear texture analysis along reptile tooth rows: complex variation with non-dietary variables

Dental microwear texture analysis (DMTA) is a powerful technique for reconstructing the diets of extant and extinct taxa. Few studies have investigated intraspecific microwear differences along with tooth rows and the influence of endogenous non-dietary variables on texture characteristics. Sampling teeth that are minimally affected by non-dietary variables is vital for robust dietary reconstructions, especially for taxa with non-occlusal (non-chewing) dentitions as no standardized sampling strategies currently exist. Here, we apply DMTA to 13 species of extant reptile (crocodilians and monitor lizards) to investigate intraspecific microwear differences along with tooth rows and to explore the influence of three non-dietary variables on exhibited differences: (i) tooth position, (ii) mechanical advantage, and (iii) tooth aspect ratio. Five species exhibited intraspecific microwear differences. In several crocodilians, the distally positioned teeth exhibited the ‘roughest' textures, and texture characteristics correlated with all non-dietary variables. By contrast, the mesial teeth of the roughneck monitor ( Varanus rudicollis ) exhibited the ‘roughest' textures, and texture characteristics did not correlate with aspect ratio. These results are somewhat consistent with how reptiles preferentially use their teeth during feeding. We argue that DMTA has the potential to track mechanical and behavioural differences in tooth use which should be taken into consideration in future dietary reconstructions.

A new method to choose the approximate function in order to determine the correlation between the imposed and the obtained clearances in FDM

Practical experiments proved that the variation of clearance between two circular pieces simultaneously manufactured by FDM, in function of different parameters has a complex variation starting from zero when the imposed clearance has a small value and being approximated by the value of the imposed clearance when the last one has great values. This observation implies that the resulted clearance may be approximated by non-linear functions for which one has to impose some frontier conditions. In this paper we discuss the conditions which have to be fulfilled by the candidate functions, considered only by polynomial ones.

A diploid assembly-based benchmark for variants in the major histocompatibility complex

Most human genomes are characterized by aligning individual reads to the reference genome, but accurate long reads and linked reads now enable us to construct accurate, phased de novo assemblies. We focus on a medically important, highly variable, 5 million base-pair (bp) region where diploid assembly is particularly useful - the Major Histocompatibility Complex (MHC). Here, we develop a human genome benchmark derived from a diploid assembly for the openly-consented Genome in a Bottle sample HG002. We assemble a single contig for each haplotype, align them to the reference, call phased small and structural variants, and define a small variant benchmark for the MHC, covering 94% of the MHC and 22368 variants smaller than 50 bp, 49% more variants than a mapping-based benchmark. This benchmark reliably identifies errors in mapping-based callsets, and enables performance assessment in regions with much denser, complex variation than regions covered by previous benchmarks.

Subspecies Variation of Daucus carota Coastal (“Gummifer”) Morphotypes (Apiaceae) Using Genotyping-by-Sequencing

Abstract—The genus Daucus is widely distributed worldwide, but with a concentration of diversity in the Mediterranean Region. The D. carota complex presents the greatest taxonomic problems in the genus. We focus on a distinctive phenotypic group of coastal morphotypes of D. carota, strictly confined to the margins to within about 0.5 km of the Mediterranean Sea and the Atlantic Ocean, which we here refer to as coastal morphotypes or D. carota subsp. “gummifer” complex. They are loosely morphologically coherent, sharing a relatively short stature, thick, broad, sometimes highly glossy leaf segments, and usually flat or convex fruiting umbels. We analyzed 288 accessions obtained from genebanks in England, France, and the USA, and an expedition to Spain in 2016, covering the Mediterranean and Atlantic coasts and Balearic Islands, where much of the gummifer complex variation occurs. Our study includes 112 accessions not examined before in this context. Genotyping-by-sequencing identified 29,041 filtered SNPs. Based on high bootstrap support from maximum likelihood and Structure analysis we highlight three main clades. The gummifer morphotypes are intercalated with members of Daucus carota subspecies carota and subspecies maximus in two of these main clades, including a clade containing accessions from Tunisia (also including D. carota subsp. capillifolius) and a clade containing accessions from western Europe (including the British Isles), southern Europe (including the Balearic Islands and the Iberian Peninsula) and Morocco. These results support five independent selections of the gummifer morphotypes in these restricted maritime environments in the Mediterranean and nearby Atlantic coasts. Daucus annuus (=Tornabenea annua) and Daucus tenuissimus (=Tornabenea tenuissima) also fall firmly within D. carota, supporting their classification as morphologically well-defined subspecies of D. carota, which are accepted here under the new combinations Daucus carota subsp. annuus and D. carota subsp. tenuissimus, respectively. Types are indicated for most of treated names, including designation of four lectotypes and three epitypes, which fix their further use.

Timing Is Everything…Or Is It? Effects of Instructed Timing Style, Reference, and Pattern on Drum Kit Sound in Groove-Based Performance

This study reports on an experiment that tested whether drummers systematically manipulated not only onset but also duration and/or intensity of strokes in order to achieve different timing styles. Twenty-two professional drummers performed two patterns (a simple “back-beat” and a complex variation) on a drum kit (hi-hat, snare, kick) in three different timing styles (laid-back, pushed, on-beat), in tandem with two timing references (metronome and instrumental backing track). As expected, onset location corresponded to the instructed timing styles for all instruments. The instrumental reference led to more pronounced timing profiles than the metronome (pushed strokes earlier, laid-back strokes later). Also, overall the metronome reference led to earlier mean onsets than the instrumental reference, possibly related to the “negative mean asynchrony” phenomenon. Regarding sound, results revealed systematic differences across participants in the duration (snare) and intensity (snare and hi-hat) of strokes played using the different timing styles. Pattern also had an impact: drummers generally played the rhythmically more complex pattern 2 louder than the simpler pattern 1 (snare and kick). Overall, our results lend further evidence to the hypothesis that both temporal and sound-related features contribute to the indication of the timing of a rhythmic event in groove-based performance.

Analysis of the Spatiotemporal Behavior of Precipitation in South Korea Based on EOF and CSEOF Analyses

In this study, EOF analysis and CSEOF analysis were applied to major ASOS precipitation data in Korea to evaluate the spatiotemporal variability of precipitation in Korea. It was concluded that both EOF and CSEOF analyses are appropriate for identifying the spatiotemporal characteristics of precipitation in Korea. In particular, the CSEOF analysis method was able to interpret the temporal, cyclic behavior of precipitation data in detail. Both EOF and CSEOF showed that the first component explained the variance of most of the raw data. From the first EOF to the third EOF, the authors identified the average precipitation characteristics in Korea, precipitation characteristics according to latitude, and the phenomenon estimated by the mountain effect. The first CSEOF was characterized by precipitation in summer and winter in Korea, the second CSEOF was characterized by latitude and local precipitation, and the third CSEOF was characterized by varied and complex variation in precipitation.