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
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
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