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Illumina / manta

Structural variant and indel caller for mapped sequencing data
GNU General Public License v3.0
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Genotype candidates provided in input VCF #9

Open ctsa opened 9 years ago

ctsa commented 9 years ago

Provide a workflow to force genotyping for all variants provided in an input VCF. For example, apply the manta candidate output from a joint trio analysis to additional family members.

Adding: @holtgrewe

crazyhottommy commented 8 years ago

I was gonna ask how did you get the genotype in your example

ctsa commented 8 years ago

Hi Ming,

The genotyping procedure is described in our pre-print. In particular section 2.3.3 from the supplement is probably a good starting point:

http://biorxiv.org/content/biorxiv/suppl/2015/08/10/024232.DC1/024232-1.pdf

This is a bit OT for this issue, so please followup with me or @x-chen directly if you have questions.