Some of these aren’t strictly filters, but weights that The post-call filtering is covered in more detail, split up into SNPīcftools mpileup includes a number of options that govern when an indel This sort of filtering is typically performed byĬommand line arguments in either bcftools mpileup or bcftools call Variant, such as specifying the minimum number of reads required toĬall an insertion. However there are times where we know we may never wish to accept a Where possible post-call filtering gives us the most flexibility as weĬan adjust the filter rules and rapidly produce a revised call set Which are then used for further filtering. Is emitted along with ancillary metrics, such as quality and depth, Pre-call filtering is where the application decides not to emit a Techniques described however can be applied to any data set if youįiltering in Bcftools is broadly broken down into two types: pre and Therefore any recommendations need to be taken cautiously. Sample with an expectation of broadly even allele frequencies and
It is important to note this guide is covering filtering a single WGS
