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Whole Genome Sequencing and structural variation identification in human..

Hello,

I have two queries regarding the structural variation identification using whole genome sequencing in human.

If you can suggest, to identify structural variation (SV) like balanced chromosomal abnormalities (BCA) what technology would be the best or good to use in whole genome sequencing (WGS): Illumina 300 bp read length technology (fragment analysis) or mate-pair technology . What would be the difference between these two technologies (advantages/disadvantages). If Illumina 300 bp read length technology would be good enough to serve the purpose here instead of mate-pair. Also cost wise which will be effective?

Also if there is any recommended GATK best practices guidelines for BCA breakpoint identification and/or any other SV identification analysis. How to analyze the data?

Thanks & regards,
Aneek

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