Filtering metrics for vcf
ManavalanG opened this issue · comments
In GitLab by @tkmamidi on Sep 30, 2021, 11:52
We're using filters to remove poor variant calls. Unfortunately, one of the variants that has been declared as solve got filtered out. This variant is not present in either of the parents vcf's. It is hard to say if it is a reliable denovo variant or a poor variant call without having bam files. Below is the variant
This variant got removed due to lower depth of 7, when >8 was used for filtering. What's interesting is that this variant is in chromosome X, which makes us wonder if the sex chromosomes need special care when applying depth filters.
This issue is specific to the CAGI6 project from the past life and is out of scope for DITTO model development. Closing this issue now.