bcftools
bcftools copied to clipboard
Option to move filter to format in merge
The filter logic in merge is really nice
-F, --filter-logic x|+ Remove filters if some input is PASS ("x"), or apply all filters ("+") [+]
but I want to suggest another option which would move the filters to a new FORMAT field. My use case for example is I have merged the VCF for four samples and would like to be able to check which samples had a filter at a position. At the moment, using "+" I just know that at least one sample had a filter, but not which sample.
If there is an alternate way of doing this I would love to know.