On the configuration doc page the section under liftover fields is TODO.
While most of the fields are self-explanatory, it would be helpful to have confirm some details on a couple of the fields. In lieu of completing the whole doc section, I've posed a couple questions here that might help to fill out some of the details for us and others and would be quicker and easier to answer than updating the configuration page ;-) We could try to read the code but it is not always clear.
number: basic
does this mean just single entry for all variants ? (alleles and genotype are clear enough)
default_type:
does this mean that all variants will have this value unless the specific variant type has this format field ?
count: 0 (or 1)
we can guess but good to confirm this.
Separate unifier_config: question
We noticed that with a custom config the unifier_config: has a default which we did not explicitly specify in the custom yaml.
drop_filtered: false
We are wondering - what is the downstream effect of drop_filtered: false. If the FILTER is non-PASS, does glnexus consider them to be true called variants ?
On the configuration doc page the section under liftover fields is TODO. While most of the fields are self-explanatory, it would be helpful to have confirm some details on a couple of the fields. In lieu of completing the whole doc section, I've posed a couple questions here that might help to fill out some of the details for us and others and would be quicker and easier to answer than updating the configuration page ;-) We could try to read the code but it is not always clear.
number: basic does this mean just single entry for all variants ? (alleles and genotype are clear enough)
default_type: does this mean that all variants will have this value unless the specific variant type has this format field ?
count: 0 (or 1) we can guess but good to confirm this.
Any other options not listed in the example ? https://github.com/dnanexus-rnd/GLnexus/wiki/Configuration
Separate unifier_config: question We noticed that with a custom config the unifier_config: has a default which we did not explicitly specify in the custom yaml.
drop_filtered: false
We are wondering - what is the downstream effect of drop_filtered: false. If the FILTER is non-PASS, does glnexus consider them to be true called variants ?
Thanks very much.