Dataset Open Access

Structural variant discovery and genotyping in next-generation sequencing data

Gilks, William


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{
  "publisher": "Zenodo", 
  "DOI": "10.5281/zenodo.159472", 
  "author": [
    {
      "family": "Gilks, William"
    }
  ], 
  "issued": {
    "date-parts": [
      [
        2016, 
        10, 
        6
      ]
    ]
  }, 
  "abstract": "<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>", 
  "title": "Structural variant discovery and genotyping in next-generation sequencing data", 
  "type": "dataset", 
  "id": "159472"
}
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