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Structural variant discovery and genotyping in next-generation sequencing data

Gilks, William


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  <dc:creator>Gilks, William</dc:creator>
  <dc:date>2016-10-06</dc:date>
  <dc:description>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

The unfiltered CNV pipleline results are lhm_gs.cnvs.raw.vcf.gz

Filtered CNV results (including removal of bad samples) are filtered.goodS.lhm_gs.cnvs.raw.vcf.gz

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

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.

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

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  <dc:identifier>https://zenodo.org/record/159472</dc:identifier>
  <dc:identifier>10.5281/zenodo.159472</dc:identifier>
  <dc:identifier>oai:zenodo.org:159472</dc:identifier>
  <dc:relation>info:eu-repo/grantAgreement/EC/FP7/280632/</dc:relation>
  <dc:relation>doi:10.5281/zenodo.654872</dc:relation>
  <dc:relation>url:https://zenodo.org/communities/drosophila</dc:relation>
  <dc:relation>url:https://zenodo.org/communities/ecfunded</dc:relation>
  <dc:relation>url:https://zenodo.org/communities/sussex_drosophila_sequencing</dc:relation>
  <dc:relation>url:https://zenodo.org/communities/william_gilks</dc:relation>
  <dc:relation>url:https://zenodo.org/communities/zenodo</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:rights>https://creativecommons.org/licenses/by/4.0/legalcode</dc:rights>
  <dc:subject>Drosophila</dc:subject>
  <dc:subject>CNV</dc:subject>
  <dc:subject>Bioinformatics</dc:subject>
  <dc:subject>Genetics</dc:subject>
  <dc:subject>Genomics</dc:subject>
  <dc:subject>NGS</dc:subject>
  <dc:title>Structural variant discovery and genotyping in next-generation sequencing data</dc:title>
  <dc:type>info:eu-repo/semantics/other</dc:type>
  <dc:type>dataset</dc:type>
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