I hope it's ok to ask this here... could anyone help a total beginner to either use LiftoverVCF in docker to remap VCF files, or set up one of the open source, user friendly VCF filtering tools?
I want to analyse my own personal WGS as I have severe health problems that may be genetic, but can't afford a full clinical service. I have some knowledge of genetics from the medical side, but am completely new to bioinformatics - and new even just to linux or containers.
I've been trying to learn as I go but keep getting stuck. So far I've tried:
Mendel MD - I'd really like to use this but my data is GRCh38, and at the moment Mendel MD only works with GRCh37. My files are too big for the NCBI remapper, even if I cut them down to one chromosome per file, so I've been trying to use LiftoverVCF instead but can't work out what I'm doing wrong.
VCF-miner - docker setup seemed to go ok but I get stuck at the final step and can't access it through a browser.
Seqr - sounds good but so far haven't been able to set up minikube or install kubectl.
BrowseVCF and VCF.Filter - set up ok but don't work well with my files and/or so user-unfriendly that effectively unusable.
I have Windows 10 with Ubuntu on the Linux Subsystem for Windows, with docker able to run through either Windows or Ubuntu.
Please - could anyone talk me through one of these?