I am analysing 18 exome sequencing samples for identification of germline variants. I separated the SNPs and Indels from the genotype.vcf file using SelectVariants and performed hard filtration as recommended here.
Now I have merged the SNPs and Indels into one file using CombineVariants and am going for genotype refinement using the trio.ped file as described here, but I am not sure if I should first remove the filtered variants (flagged at the variant filtration stage) before performing the refinement. In some tutorials I see that SelectVariants with --excludeFiltered is used in some tutorials VariantFiltration output is directly used for refinement.
Is this "exclude filtered" step essential or recommended?
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