Structural variant discovery and genotyping in next-generation sequencing data

Gilks, William (2016) Structural variant discovery and genotyping in next-generation sequencing data. [Dataset]

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Abstract

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

Item Type: Dataset
Additional Information: DOI:10.5281/zenodo.159472
Keywords: Genetics, data visualisation, R, ggplot, genomics, structural variation, copy-number variation, Drosophila.
Schools and Departments: School of Life Sciences > Evolution, Behaviour and Environment
Subjects: Q Science > QH Natural history > QH0301 Biology > QH0426 Genetics
Q Science > QH Natural history > QH0301 Biology > QH0426 Genetics > QH0438.4 Special aspects of the subject as a whole, A-Z
Q Science > QH Natural history > QH0301 Biology > QH0426 Genetics > QH0447 Genes. Alleles. Genome
Q Science > QH Natural history > QH0301 Biology > QH0426 Genetics > QH0470.A-Z Experimental organisms, A-Z
Q Science > QH Natural history > QH0301 Biology > QH0426 Genetics > QH0470.A-Z Experimental organisms, A-Z > QH0470.D7 Drosophila
Q Science > QH Natural history > QH0301 Biology > QH0426 Genetics > QH0460 Mutations
Related URLs:
Depositing User: William Gilks
Date Deposited: 15 Nov 2016 13:10
Last Modified: 15 Nov 2016 13:13
URI: http://sro.sussex.ac.uk/id/eprint/65472
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Project NameSussex Project NumberFunderFunder Ref
2Sexes_1Genome: Sex-specific genetic effects on fitness and human diseaseG0781EUROPEAN UNION2011-STG280632