Tag: ANGSD

No @hd header returned in sam file when running bwa mem

No @hd header returned in sam file when running bwa mem 1 Hello, I produced sam files with the below command: bwa mem -M -t 10\ IndexedReference\ ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz\ 2> ${sample}_bwa.err > ${sample}.sam` The resulting sam file doesn’t have an @hd header. Example output of samtools view: samtools view -H…

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POOLPARTY2: An integrated pipeline for analyzing pooled or indexed low coverage whole genome sequencing data to discover the genetic basis of diversity

POOLPARTY2: An integrated pipeline for analyzing pooled or indexed low coverage whole genome sequencing data to discover the genetic basis of diversity Abstract Whole genome sequencing data allow survey of variation from across the genome, reducing the constraint of balancing genome sub-sampling with recombination rates and linkage between sampled markers…

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course- Population genomic inference from low-coverage whole-genome sequencing data

Dear all, registration is now open for the 4th edition of the course “Population genomic inference from low-coverage whole-genome sequencing data” Dates: online, 2-5 October 2023 Instructors: Dr. Nina Overgaard Therkildsen (Cornell University, USA) Dr. Tyler Linderoth (University of California Berkeley, USA), Dr. Arne Jacobs (University of Glasgow, UK) and…

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Dryad | Data — Whole genome sequencing (WGS) data from invasive pine sawfly Diprion similis

Biological introductions are unintended “natural experiments” that provide unique insights into evolutionary processes. Invasive phytophagous insects are of particular interest to evolutionary biologists studying adaptation, as introductions often require rapid adaptation to novel host plants. However, adaptive potential of invasive populations may be limited by reduced genetic diversity—a problem known…

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How to get BEAGLE files from VCF with angsd?

How to get BEAGLE files from VCF with angsd? 0 Hello, I want to output genotype likelihood BEAGLE file from VCF file with angsd, in order to use them in pcangsd later. But with the following command I obtain an error message. angsd \ -GL 2 \ -out output_file \…

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doing PBS(population branch statistics) in ANGSD

doing PBS(population branch statistics) in ANGSD 0 Hi everyone, i am trying to do a Population branch statistic on my data i have done the first step where i calculate saf, now i need to do the second step calculating 2dsfs. when i submit the script on the cluster. I…

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Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers

Prüfer, K. et al. A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia. Nat. Ecol. Evol. 5, 820–825 (2021). Article  PubMed  PubMed Central  Google Scholar  Hajdinjak, M. et al. Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry. Nature 592, 253–257…

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Co-diversification of an intestinal Mycoplasma and its salmonid host

Alberdi A, Aizpurua O, Bohmann K, Zepeda-Mendoza ML, Gilbert MTP. Do vertebrate gut metagenomes confer rapid ecological adaptation? Trends Ecol Evol 2016;31:689–99. Article  PubMed  Google Scholar  Groussin M, Mazel F, Alm EJ. Co-evolution and co-speciation of host-gut bacteria systems. Cell Host Microbe. 2020;28:12–22. Article  CAS  PubMed  Google Scholar  Alberdi A,…

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convert beagle genotypes to vcf

convert beagle genotypes to vcf 0 Hi, I have a phased beagle file which I generated through Angsd v0.935. I would like to use the beagle utility program beagle2vcf.jar. However I keep getting this error: java -jar beagle2vcf.jar rs markers bgl_comb ? > vcf Exception in thread “main” java.lang.IllegalArgumentException: Alleles…

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Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes

Luo, M. C. et al. Synteny analysis in rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials. BMC Genom. 16, 707 (2015). Article  Google Scholar  Martinez-Garcia, P. J. et al. The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of…

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arlequin SFS output

arlequin SFS output 1 Hi, I’ve converted a ped file to arlequin using pgdspider. As I don’t have the ancestral state, I haven’t done the numeric conversion. Yet, when I ask arlequin to output the SFS, it returns MAF files, i.e., theoretically, the folded SFS. When I look into this…

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ANGSD | FSU Research Computing Center

Introduction ANGSD is a software for analyzing next generation sequencing data intended for use with mapped reads to imputed genotype probabilities. ANGSD can work with BAM files but is not meant for manipulating them. SAMTools is best for that. ANGSD is ideal for use with low to medium depth genomic…

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Contrasting levels of hybridization across the two contact zones between two hedgehog species revealed by genome-wide SNP data

Ai H, Fang X, Yang B, Huang Z, Chen H, Mao L et al. (2015) Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing. Nat Genet 47:217–225 CAS  PubMed  Article  Google Scholar  Alexander DH, Lange K (2011) Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC…

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South-to-north migration preceded the advent of intensive farming in the Maya region

Moreno-Mayar, J. V. et al. Early human dispersals within the Americas. Science 362, eaav2621 (2018). ADS  PubMed  Google Scholar  Posth, C. et al. Reconstructing the deep population history of Central and South America. Cell 175, 1185–1197.e22 (2018). CAS  PubMed  PubMed Central  Google Scholar  Raghavan, M. et al. Genomic evidence for…

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Genomic variation from an extinct species is retained in the extant radiation following speciation reversal

Vamosi, J. C., Magallon, S., Mayrose, I., Otto, S. P. & Sauquet, H. Macroevolutionary patterns of flowering plant speciation and extinction. Annu. Rev. Plant Biol. 69, 685–706 (2018). CAS  PubMed  Google Scholar  Rhymer, J. M. & Simberloff, D. Extinction by hybridization and introgression. Annu. Rev. Ecol. Syst. 27, 83–109 (1996)….

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GitHub – e-jorsboe/ANGSD-asso-scripts

GitHub – e-jorsboe/ANGSD-asso-scripts You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session. Read more here: Source link

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Regions File Format – ANGSD-wrapper/angsd-wrapper Wiki

ANGSD-wrapper prefers the regions file to be formatted as chr_name:start_position-end_position. Below, we will create a toy BED file as an example and show how we can go from BED file format to ANGSD-wrapper’s regions file format. Create toy BED file Let’s create an example BED file. You can run the…

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