evaluate `GLnexus` for joint variant calling

[matthdsm]

Description of feature

https://github.com/dnanexus-rnd/GLnexus

[matthdsm]

Anything to drop GATK!

[nvnieuwk]

This might be a good alternative when adding deepvariant. This tool seems to be optimized on deepvariant output :)

[matthdsm]

Some further research shows GLnexus is deprecated and no longer maintained, with some serious issues still open

xref:

• (DP) Depth value being incorrectly set to 0 for calls  dnanexus-rnd/GLnexus#286
• Replace GLNexus genomic-medicine-sweden/nallo#398
• Population calling | joint calling | ensemble calling nf-core/sarek#868

[nvnieuwk]

[matthdsm]

cfr PacBio rep

We hebben de parameters van DeepVariant een klein beetje veranderd om dit probleem te voorkomen. De WDL gebruikt de DeepVariant_unfiltered configuratie met één aanpassing. De minimale diepte moet minstens 1 read zijn (required_dp: 1, zie: [https://github.com/PacificBiosciences/wdl-common/blob/01f15270d617a6082960cad3f1d05ea610f15ba9/wdl/tasks/glnexus.wdl#L54](https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FPacificBiosciences%2Fwdl-common%2Fblob%2F01f15270d617a6082960cad3f1d05ea610f15ba9%2Fwdl%2Ftasks%2Fglnexus.wdl%23L54&data=05%7C02%7CMatthias.DeSmet%40ugent.be%7Cd658be0e2c584605cffd08dd701fd480%7Cd7811cdeecef496c8f91a1786241b99c%7C1%7C0%7C638790004201424398%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=FvPWbWKSWoKHheFAFhPkFbzJDbpdpbNDnzOSibWj%2F0M%3D&reserved=0)). Hierdoor worden er geen 0/0 calls gemaakt zonder reads.