change freebayes min depth param

[sanjaynagi]

This needs changing to 4 ideally as previous studies shown variant calling accurate above this level. already we have missingness filters high so this probably wont make much difference.

[sanjaynagi]

Related -

Should we have a filter for:

• Sites of poor mapping quality?
• Sites at homopolymers
• Sites at exon-intron junctions

and how many SNPs will this remove?

[sanjaynagi]

We should also potentially use a maximum depth filter within freebayes, we have --use-best-n-alleles which may do the same job, however.