Vep : MNP phased genotype
I would like to know what is the best way to annotate a vcf taking into account the mnp. I specify that it is about a vcf with phased genotype.
For annotations i used ensembl vep. I saw that there is in the vep package, haplosaurus which annotates according to mnp, but how to combine vep and haplosaurus? I mean to have all the info provided by vep (including plugins) but in addition the mnp info?
I take this opportunity to ask another question about vep: to annotate a genome, so that it doesn’t take too long, I don’t want to put all the annotations on all the variants. in particular the slowest info to calculate such as the splicing I would like to put it only on the variants present in the genes and with a sufficiently low frequency in gnomad. I therefore thought of making a first annotations then filtering to obtain two vcf one with the variants of which I want more info and the other not. Then add the new annotations and finally merge the two vcf. Is this the right method? Merge two vcf which will not wear exactly the same fields in csq is not likely to pose a problem?
Thanks in advance.
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