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SelectVariants exclude non-variant sites after GenotypeGVCF
I merged 40 individual gvcf files with CombineGVCFs and set the Genotype with GenotypeGVCF.
After that, I want to filter out those sites which have no SNPs or INDEL in all the samples.
Is it appropriate to filter these sites out with SelectVariants?
Will it keep the sites which is not only lack of data in some of the sample but the homozygote in some other samples ?
What does the SelectVariants --exclude-non-variants depend on ? Does it depend on the sites which ALT exist ?