STAR genomeConsensusFile description

Question

[chasem]

In the STAR 2.7 docs, this setting is defined:

14.4 Genome Parameters
...
--genomeConsensusFile
default: -
string: VCF file with consensus SNPs (i.e. alternative allele is the major
(AF>0.5) allele)

But I am unsure of what this looks like, exactly. If there are for instance 4000 samples, presumably I wouldn't need to keep all of those samples in the VCF after filtering for sites with minor allele freq > .5? Would one just randomly select a sample to keep, in this case?

A follow on to this -- how does using the --genomeConsensusFile affect --varVCFfile, which are variants for a specific sample, if at all? Is it unnecessary to use genomeConsensusFile if using varVCFfile?

Finally, which one of these (maybe both? maybe neither?) affect behavior when seeting --waspOutputMode?

14.24 WASP parameters
--waspOutputMode
default: None
string: WASP allele-specific output type. This is re-implemenation of the
original WASP mappability filtering by Bryce van de Geijn, Graham McVicker,
Yoav Gilad & Jonathan K Pritchard. Please cite the original WASP paper:
Nature Methods 12, 1061–1063 (2015),
https://www.nature.com/articles/nmeth.3582 .
SAMtag
add WASP tags to the alignments that pass WASP filtering