Dataset Open Access

Structural variant discovery and genotyping in next-generation sequencing data

Gilks, William


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    <subfield code="a">&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;

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