Issues in vca_reg pipe

[ilyakichigin]

-----annotate-region-variants sometimes repeats variants inside one transcript

regpos.count.txt file has Intergenic, splicesite, upstream, downstream regions doubled.

Add indel realignment

[amakunin]

Also: assign read groups e t.c. upon alignment.

Add optional PCR duplicate removal.

Variant densities are impractical.

Thus, implement new variant calling pipeline as an alternative to the old one.