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Structural variant discovery and genotyping in next-generation sequencing data

Gilks, William


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{
  "description": "<p>Code, logs, data, and summaries for detection and genotyping of genomic structural variants in the D.melanogaster Sussex LHM hemiclones (and one in-house reference line individual), using Genomestrip/2.0</p>\n\n<p>The unfiltered CNV pipleline results are lhm_gs.cnvs.raw.vcf.gz</p>\n\n<p>Filtered CNV results (including removal of bad samples) are filtered.goodS.lhm_gs.cnvs.raw.vcf.gz</p>\n\n<p>The file uploaded to NCBI dbVAR (which comprises of the filtered CNVs and indels &gt;50bp from the HaplotypeCaller method) is lhm_sx16.dbVAR.vcf.gz</p>\n\n<p>The NCBI dbVAR accession number is nstd134. Code, logs and summary data are in the zipped archives, named accordingly. The archive reference_data.zip contains additional input files required for Genomestrip, including a shell script for making some of them. The file gstrip_lhm_RG_bams.list is also an input for Genomestrip, indicating bam file names and paths.</p>\n\n<p>The pre-print manuscript for this data is available on biorxiv: \"Whole genome resequencing of a laboratory-adapted Drosophila melanogaster population sample\" http://biorxiv.org/content/early/2016/10/17/081554 doi: http://dx.doi.org/10.1101/081554</p>\n\n<p>\u00a0</p>", 
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "University of Sussex", 
      "@type": "Person", 
      "name": "Gilks, William"
    }
  ], 
  "url": "https://zenodo.org/record/159472", 
  "datePublished": "2016-10-06", 
  "keywords": [
    "Drosophila", 
    "CNV", 
    "Bioinformatics", 
    "Genetics", 
    "Genomics", 
    "NGS"
  ], 
  "@context": "https://schema.org/", 
  "distribution": [
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    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/a249d0fc-7e4b-4ab2-a1ef-2ae17f8eef0c/gs_code.zip", 
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    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/a249d0fc-7e4b-4ab2-a1ef-2ae17f8eef0c/gs_logs.zip", 
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    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/a249d0fc-7e4b-4ab2-a1ef-2ae17f8eef0c/gs_reference_data.zip", 
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    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/a249d0fc-7e4b-4ab2-a1ef-2ae17f8eef0c/gs_summary_data.zip", 
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    {
      "contentUrl": "https://zenodo.org/api/files/a249d0fc-7e4b-4ab2-a1ef-2ae17f8eef0c/gstrip_lhm_RG_bams.list", 
      "encodingFormat": "list", 
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    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/a249d0fc-7e4b-4ab2-a1ef-2ae17f8eef0c/lhm_gs.cnvs.raw.vcf.gz", 
      "encodingFormat": "gz", 
      "@type": "DataDownload"
    }, 
    {
      "contentUrl": "https://zenodo.org/api/files/a249d0fc-7e4b-4ab2-a1ef-2ae17f8eef0c/lhm_sx16.dbVAR.vcf.gz", 
      "encodingFormat": "gz", 
      "@type": "DataDownload"
    }
  ], 
  "identifier": "https://doi.org/10.5281/zenodo.159472", 
  "@id": "https://doi.org/10.5281/zenodo.159472", 
  "@type": "Dataset", 
  "name": "Structural variant discovery and genotyping in next-generation sequencing data"
}
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