Add CHM13 VEP documentation

[ljwharbers]

Description of feature

Add documentation how to use VEP with CHM13.

1. Download VEP cache
   https://www.ensembl.info/2024/08/09/cool-stuff-ensembl-vep-can-do-supporting-alternative-human-assemblies/
   curl -O https://ftp.ensembl.org/pub/rapid-release/species/Homo_sapiens/GCA_009914755.4/ensembl/variation/2022_10/indexed_vep_cache/Homo_sapiens-GCA_009914755.4-2022_10.tar.gz tar xzf Homo_sapiens-GCA_009914755.4-2022_10.tar.gz

2. Add the following parameters

--vep_cache_version 107
--vep_cache /path/to/downloaded_cache

Rest should be correct if using iGenomes. If not using iGenomes. Also include:

 --vep_genome T2T-CHM13v2.0
 --vep_species homo_sapiens_gca009914755v4

[ljwharbers]

Perhaps include the versions for hg38 and CHM13 and maybe a vep cache thats on github lfs for CHM13. That way people don't have to download and specify their own.