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Old 08-09-2016, 12:24 PM   #1
Location: Boulder, Co

Join Date: Oct 2010
Posts: 13
Default Trio Structural variant genotyping

I'm working with trio structural variant calling from Illumina paired-end WGS. I've called variants using LumpySV, and I have both bedpe and vcf files for mother, father, and child.

I now want to genotype these variants:
Both via heterozygous, homozygous, hemizygous, as well as based on inheritance patterns, i.e. Recessive, de novo

Then I want to take them through an annotation vs. genes, regulatory regions, DGV, etc.

If anyone has a pipeline set up for this or can point me to the correct place that would be very helpful.

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Old 08-16-2016, 01:10 AM   #2
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Location: Denmark

Join Date: Jul 2012
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Depending on the size of structural variants genotyping does not have a straightforward solution. Pindel can give you genotypes for smaller events (upto 100bp) but with larger events (> 1kb), even defining boundaries is a bit of a challenge, so as it is there is no out of the box solution. In the past I've used Bedtools to add gene annotation and roughly genotype the large SVs.
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