revise normal depth cutoff for variants

[anoronh4]

We are currently using a hard cutoff for normal read count of alt alleles:

tempo/containers/vcf2maf/filter-somatic-maf.R

Lines 35 to 36 in 499ee2a

	parser$add_argument('-nc', '--normal-count', type = 'integer', required = FALSE,
	default = 3, help = 'Normal variant read support cut-off [default %(default)s]')

With higher depth sequencing in the normal, we see that known mutations are filtered out as normal alt counts rise, even though the frequency is not necessarily high.

There are other hard cutoffs in this script and filter-vcf.py and we should take a look at them too.

[anoronh4]

based on a group discussion we basically don't want to go in the direction of using a proportion and want to keep using hard cut-offs. For any new assays such as IMPACT, we will use the cutoffs from other pipelines as guidance such as argos.