Trio Structural variant genotyping

P-Richmond · 08-09-2016, 12:24 PM

Hello,
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.

Thanks,
Phil

vivek_ · 08-16-2016, 01:10 AM

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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08-09-2016, 12:24 PM	#1
P-Richmond Member Location: Boulder, Co Join Date: Oct 2010 Posts: 13	Trio Structural variant genotyping Hello, 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. Thanks, Phil

08-16-2016, 01:10 AM	#2
vivek_ PhD Student Location: Denmark Join Date: Jul 2012 Posts: 164	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.