Add mBAF analysis step to the Hisat/StringTie pipeline

[Nicklas Nordborg]

The Hisat/StringTie pipeline should be extended with a mBAF analysis step. The idea is that mBAF values that differ from 0.5 or 1 is an indication of tumor cells in the sequenced material.

The first part is to analyse (with HaplotypeCaller) the allele frequencies for a larger number of SNP:s. The result is a VCF file that should be attached to the alignment (we could for example call it mbaf_genotype.vcf).

When we have the file it is possible to extract data and calculate mBAF average values for most chromosome arms and some other minor regions. The mBAF values can be compared to those for a "normal" reference group. The exact details of this comparison has not yet been settled.

Implementation wise:

• We should use an item list as the source list for the mBAF analysis.
• The "auto-confirm" rules for Hisat -> StringTie should be applied also for the mBAF analysis.

NOTE! Comments and code was added to ticket #1058 by accident! Please look there for more information.