Dataset Open Access

Structural variant discovery and genotyping in next-generation sequencing data

Gilks, William

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 >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

 

Files (488.4 MB)
Name Size
filtered.goodS.lhm_gs.cnvs.raw.vcf.gz
md5:d7b81fb0b59b527f062af94ac5381a1c 		1.2 MB Download
gs_code.zip
md5:a8df72c02e9a7f908848e893523a9df2 		9.4 kB Download
gs_logs.zip
md5:c61937f4f2573d0f880246d25cb4729e 		112.9 MB Download
gs_reference_data.zip
md5:a682f3d7a580c4041121f612e8930713 		336.5 MB Download
gs_summary_data.zip
md5:cec11ea6835f70d11d395fed3b8103d3 		18.2 kB Download
gstrip_lhm_RG_bams.list
md5:f123d38165a7bd5e9802b75e0d85de2c 		10.0 kB Download
lhm_gs.cnvs.raw.vcf.gz
md5:1513f404cfa18cf172010fd9150e2703 		32.9 MB Download
lhm_sx16.dbVAR.vcf.gz
md5:e2d063597591d6b18a39a7d0c6ac4784 		4.9 MB Download
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Publication date:
October 6, 2016
DOI:
10.5281/zenodo.159472

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Keyword(s):
Drosophila CNV Bioinformatics Genetics Genomics NGS
Grants:
European Commission:
  • 2SEXES_1GENOME - Sex-specific genetic effects on fitness and human disease (280632)
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License (for files):
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