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Structural variant discovery and genotyping in next-generation sequencing data

Gilks, William


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  <identifier identifierType="DOI">10.5281/zenodo.159472</identifier>
  <creators>
    <creator>
      <creatorName>Gilks, William</creatorName>
      <givenName>William</givenName>
      <familyName>Gilks</familyName>
      <affiliation>University of Sussex</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Structural variant discovery and genotyping in next-generation sequencing data</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2016</publicationYear>
  <subjects>
    <subject>Drosophila</subject>
    <subject>CNV</subject>
    <subject>Bioinformatics</subject>
    <subject>Genetics</subject>
    <subject>Genomics</subject>
    <subject>NGS</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2016-10-06</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/159472</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.654872</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/drosophila</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/ecfunded</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/sussex_drosophila_sequencing</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/william_gilks</relatedIdentifier>
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  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;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&lt;/p&gt;

&lt;p&gt;The unfiltered CNV pipleline results are lhm_gs.cnvs.raw.vcf.gz&lt;/p&gt;

&lt;p&gt;Filtered CNV results (including removal of bad samples) are filtered.goodS.lhm_gs.cnvs.raw.vcf.gz&lt;/p&gt;

&lt;p&gt;The file uploaded to NCBI dbVAR (which comprises of the filtered CNVs and indels &amp;gt;50bp from the HaplotypeCaller method) is lhm_sx16.dbVAR.vcf.gz&lt;/p&gt;

&lt;p&gt;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.&lt;/p&gt;

&lt;p&gt;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&lt;/p&gt;

&lt;p&gt; &lt;/p&gt;</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/FP7/280632/">280632</awardNumber>
      <awardTitle>Sex-specific genetic effects on fitness and human disease</awardTitle>
    </fundingReference>
  </fundingReferences>
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