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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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the problem of genetype missing rate #320

Open zhangjijin opened 4 years ago

zhangjijin commented 4 years ago

Hi Ryan.

I call SV for each samples ,when i merge all the sample's VCF ,the problem occurs. The most GT is ./. ,the gentype missing rate is very high (80%~90%) My data's depth is average 10 X . What should i do ?

ryanlayer commented 4 years ago

You need to find the full set of SVs across all samples (typically called a sites vcf) then genotype all samples for this vcf with svtyper, then merge. smoove has made this much easier

https://github.com/brentp/smoove

On Nov 20, 2019, at 12:07 AM, jijizhang notifications@github.com wrote:

 Hi Ryan.

I call SV for each samples ,when i merge all the sample's VCF ,the problem occurs. The most GT is ./. ,the gentype missing rate is very high (80%~90%) My data's depth is average 10 X . What should i do ?

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