Opened 2 years ago

Closed 2 years ago

Last modified 2 years ago

#1068 closed task (fixed)

Add mBAF analysis step to the Hisat/StringTie pipeline

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.20
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by 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.

Change History (4)

comment:1 Changed 2 years ago by Nicklas Nordborg

Milestone: Reggie v4.xReggie v4.20
Status: newassigned

comment:2 Changed 2 years ago by Nicklas Nordborg

Description: modified (diff)
Resolution: fixed
Status: assignedclosed

comment:3 Changed 2 years ago by Nicklas Nordborg

Description: modified (diff)

comment:4 Changed 2 years ago by Nicklas Nordborg

(In [5064]) References #1068: Add mBAF analysis step to the Hisat/StringTie? pipeline

File links should be created 'soft' links so that they can be easier removed or replaced if we want to.

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