Update VCF filtration and QC

[yashpatel6]

For the filtration script, it seems like only the last sample is actually processed, so if we input --tumour sample1 --tumour sample2 --tumour sample3, only sample3 is kept. The preceding --tumour inputs are ignored so the script probably will require an update.

Yeah, I've checked the command and it wouldn't work properly. We might want to drop the script and add a simple filtering process using BCF/VCFtools (e.g. https://github.com/uclahs-cds/pipeline-call-sSV/blob/main/pipeline/modules/bcftools.nf) and use RTGtool for QC instead.

Originally posted by @tyamaguchi-ucla in #61 (comment)