Files for "Inheritance of somatic mutations by animal offspring"

Genotypes of acroporid corals were converted into a variant call format (vcf) (n = 1898 samples) using the Standard Tools for Acroporid Genotyping workflow (coralsnp.science.psu.edu/galaxy). The "STAGdb_04Jan2022.vcf" file was used to detect somatic mutations in select parent and offspring samples of Acropora palmata from Curacao. The "Mixed_Samples.vcf" file was used to compare genotyping results of 'pure' DNA vs. 'mixed' DNA of two A. palmata samples. These vcf files can be used with code available here and at: https://github.com/skitchen19/Acropora_Mutation_Vasquez_Kitchen_et_al.

Citation

Kitchen, Sheila; Baums, Iliana; Conn, Trinity (2022). Files for "Inheritance of somatic mutations by animal offspring" [Data set]. Scholarsphere.

Files

Metadata

Work Title Files for "Inheritance of somatic mutations by animal offspring"
Access
Open Access
Creators
  1. Sheila Kitchen
  2. Iliana Baums
  3. Trinity Conn
Keyword
  1. Acropora palmata
  2. SNP
  3. Genotype
  4. Somatic mutation
License CC BY-NC 4.0 (Attribution-NonCommercial)
Work Type Dataset
Publication Date February 17, 2022
Subject
  1. Biology
Language
  1. English
Geographic Area
  1. Curacao
  2. Florida
Related URLs
Deposited February 17, 2022

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Work History

Version 1.0.0
published

  • Created
  • Added Creator Sheila Kitchen
  • Added Creator Iliana Baums
  • Added Creator Trinity Conn
  • Updated Description Show Changes
    Description
    • Genotypes of acroporid corals converted into a variant call format (vcf) file and merged with other database samples at the time (n = 1898 in total). This file was used for detecting somatic mutations in parent and offspring sample of Acropora palmata.
    • This vcf file is to be used with code available at: https://github.com/skitchen19/Acropora_Mutation_Vasquez_Kitchen_et_al.
    • Genotypes of acroporid corals converted into a variant call format (vcf) file and merged with other database samples at the time (n = 1898 in total). The STAGdb_04Jan2022.vcf file were used for detecting somatic mutations in parent and offspring sample of Acropora palmata. The Mixed_Samples.vcf file was for comparing genotyping results of 'pure' vs. mixtures of DNA of two A. palmata samples.
    • These vcf files can be used with code available at: https://github.com/skitchen19/Acropora_Mutation_Vasquez_Kitchen_et_al.
  • Updated Description Show Changes
    Description
    • Genotypes of acroporid corals converted into a variant call format (vcf) file and merged with other database samples at the time (n = 1898 in total). The STAGdb_04Jan2022.vcf file were used for detecting somatic mutations in parent and offspring sample of Acropora palmata. The Mixed_Samples.vcf file was for comparing genotyping results of 'pure' vs. mixtures of DNA of two A. palmata samples.
    • These vcf files can be used with code available at: https://github.com/skitchen19/Acropora_Mutation_Vasquez_Kitchen_et_al.
    • These vcf files can be used with code available here and at: https://github.com/skitchen19/Acropora_Mutation_Vasquez_Kitchen_et_al.
  • Added Mixed_Samples.vcf
  • Added Mixes_Sampinfo.xlsx
  • Added CNV_analysis.R
  • Added extractGentoype_idMutations.R
  • Added Genetic_Dist_Het_Recombination_array.R
  • Added BAF_LRR_plots_per_scaffold.R
  • Added apalm_list.txt
  • Added smutations.txt
  • Added heterozygosity.csv
  • Added Axiom_AcropSNP_coral_Annotation.r1.csv
  • Added STAGdb_04Jan2022.vcf
  • Added popInfo_STAGdb_04Jan2022.tabular
  • Updated Publisher, Description, License Show Changes
    Publisher
    • bioRxiv
    Description
    • Genotypes of acroporid corals converted into a variant call format (vcf) file and merged with other database samples at the time (n = 1898 in total). The STAGdb_04Jan2022.vcf file were used for detecting somatic mutations in parent and offspring sample of Acropora palmata. The Mixed_Samples.vcf file was for comparing genotyping results of 'pure' vs. mixtures of DNA of two A. palmata samples.
    • Genotypes of acroporid corals converted into a variant call format (vcf) (n = 1898 samples). The STAGdb_04Jan2022.vcf file was used to detect somatic mutations in select parent and offspring samples of Acropora palmata from Curacao. The Mixed_Samples.vcf file was used to compare genotyping results of 'pure' DNA vs. 'mixed' DNA of two A. palmata samples.
    • These vcf files can be used with code available here and at: https://github.com/skitchen19/Acropora_Mutation_Vasquez_Kitchen_et_al.
    License
    • https://creativecommons.org/licenses/by-nc/4.0/
  • Published
  • Updated
  • Updated

Version 1.0.0
published

  • Created
  • Updated Work Title Show Changes
    Work Title
    • VCF file for "Inheritance of somatic mutations by animal offspring"
    • Files for "Inheritance of somatic mutations by animal offspring"
  • Published
  • Updated
  • Updated

Version 1.0.0
published

  • Created
  • Updated Description Show Changes
    Description
    • Genotypes of acroporid corals converted into a variant call format (vcf) (n = 1898 samples). The STAGdb_04Jan2022.vcf file was used to detect somatic mutations in select parent and offspring samples of Acropora palmata from Curacao. The Mixed_Samples.vcf file was used to compare genotyping results of 'pure' DNA vs. 'mixed' DNA of two A. palmata samples.
    • Genotypes of acroporid corals were converted into a variant call format (vcf) (n = 1898 samples) using the Standard Tools for Acroporid Genotyping workflow (coralsnp.science.psu.edu/galaxy). The "STAGdb_04Jan2022.vcf" file was used to detect somatic mutations in select parent and offspring samples of Acropora palmata from Curacao. The "Mixed_Samples.vcf" file was used to compare genotyping results of 'pure' DNA vs. 'mixed' DNA of two A. palmata samples.
    • These vcf files can be used with code available here and at: https://github.com/skitchen19/Acropora_Mutation_Vasquez_Kitchen_et_al.
  • Published
  • Updated
  • Updated

Version 1.0.0
published

  • Created
  • Updated Description Show Changes
    Description
    • Genotypes of acroporid corals were converted into a variant call format (vcf) (n = 1898 samples) using the Standard Tools for Acroporid Genotyping workflow (coralsnp.science.psu.edu/galaxy). The "STAGdb_04Jan2022.vcf" file was used to detect somatic mutations in select parent and offspring samples of Acropora palmata from Curacao. The "Mixed_Samples.vcf" file was used to compare genotyping results of 'pure' DNA vs. 'mixed' DNA of two A. palmata samples.
    • Genotypes of acroporid corals were converted into a variant call format (vcf) (n = 1898 samples) using the Standard Tools for Acroporid Genotyping workflow (coralsnp.science.psu.edu/galaxy). The "STAGdb\_04Jan2022.vcf" file was used to detect somatic mutations in select parent and offspring samples of Acropora palmata from Curacao. The "Mixed\_Samples.vcf" file was used to compare genotyping results of 'pure' DNA vs. 'mixed' DNA of two A. palmata samples.
    • These vcf files can be used with code available here and at: https://github.com/skitchen19/Acropora_Mutation_Vasquez_Kitchen_et_al.
  • Published
  • Updated
  • Updated

Version 5
published

  • Created
  • Updated Geographic Area Show Changes
    Geographic Area
    • Curacao
    • Curacao, Florida
  • Deleted extractGentoype_idMutations.R
  • Deleted apalm_list.txt
  • Added script_input_files.zip
  • Added extractGentoype_idMutations.R
  • Added raw_CEL_files.zip
  • Deleted heterozygosity.csv
  • Deleted smutations.txt
  • Published
  • Updated Source, Keyword, Subject, and 4 more Show Changes
    Source
    • Iliana Baums lab
    Keyword
    • Acropora palmata, SNP, genotype, somatic mutation
    • Acropora palmata, SNP, Genotype, Somatic mutation
    Subject
    • biology
    • Biology
    Publisher
    • bioRxiv
    Publisher Identifier (DOI)
    • https://doi.org/10.1101/2020.10.19.345538
    Related URLs
    • https://www.biorxiv.org/content/10.1101/2020.10.19.345538v1
    • https://doi.org/10.1126/sciadv.abn0707, https://github.com/skitchen19/Acropora_Mutation_Vasquez_Kitchen_et_al, coralsnp.science.psu.edu/galaxy, https://doi.org/10.1101/2020.10.19.345538
    Semantic Version
    • 1.0.0
  • Updated Related URLs Show Changes
    Related URLs
    • https://doi.org/10.1126/sciadv.abn0707, https://github.com/skitchen19/Acropora_Mutation_Vasquez_Kitchen_et_al, coralsnp.science.psu.edu/galaxy, https://doi.org/10.1101/2020.10.19.345538
    • https://doi.org/10.1126/sciadv.abn0707, https://github.com/skitchen19/Acropora_Mutation_Vasquez_Kitchen_et_al, https://coralsnp.science.psu.edu/galaxy, https://doi.org/10.1101/2020.10.19.345538
  • Updated