MarViN like MVN call for large SV

Illumina / MarViN

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MarViN like MVN call for large SV #3

Open Jordi-V opened 5 years ago

Jordi-V commented 5 years ago

Dear all,

I read the paper which is involved MarVin, but I have a question only just to clarify me...

MVN call in 1000 Genomes or GoNL was used in order to phase large SV, it not sense the type of SV is phased... So I just want to know if MarVin is checked by this purpose and I want to know if it is possible use the MarVin for this purpose and if it does better than MVN call.

Thanks for your time

Jordi

jaredo commented 5 years ago

Hi Jordi.

For 1000G, MVNcall used the phased small variants as a scaffold for conditioning when imputing the large SVs. MarVin does not have this scaffolding functionality, it just takes a set of genotype likelihoods and refines them to hard genotypes using LD information.

I hope that is helpful.

Jared