Tag: ANGSD

How to compute Hudson’s/Bhatia’s FST in R OR with vcf? 1 Hi everyone, How can I compute hierarchical Fst with Bhatia’s/Hudson’s estimator using a vcf as input? My data is structured like this: there are individuals within sampling sites, and sampling sites within groups. My vcfs contain SNP data (~1000…

ANGSD beagle generation returning empty file 0 Hello Biostars community, I am struggling quite a bit with ANGSD these days as it seems that no code I provide to the machine is working as intended. I want now to produce a beagle file but the following script is returning me…

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Ethics We confirm our research complies with all relevant ethical regulations and was approved by the animal ethics committee of the School of Biology at the University of St Andrews on 26 July 2018 www.st-andrews.ac.uk/research/environment/committees/awerb/. The three new contemporary dolphin samples analysed in this study were collected under the relevant…

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…

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…

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…

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…

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 \…

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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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,…

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…

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…

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…

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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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

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…