1.16.3

General:

• bug fixes from bug reports, mainly germline;
• 2 issues fixed (centromere coordinate, genes output)
• fixed the problem when <= 2 males were in the cohort

1.16.2

General:

• short-options removed (opt-parse package changed)
• updated docs

Germline:

• fixed mosaicism

Somatic:

• added flag 'complexTumor'

1.16.1

General:

• removed unnecessary parallelization

Germline:

• changed header

Somatic:

• bugfixes
• QC parameters (FDR)
• new baseline procedure

1.16.0

Major changes in somatic mode:

• changed procedure of baseline detection
• modified QC control
• additional QC metrics reported in header

Minor changes to germline mode:

• updated covariance calculation for overlapping input target regions
• re-formatted QC header

1.15.0

Major changes in somatic mode. Allele specific calling implemented. New QC.

1.14.1

Minor release: output was reformatted (QC lines were splitted, values rounded to human-readable length of decimals, etc)

1.14.0

Somatic:
-bugfixes
-new procedure for SNVs available for usage

Germline:
-super-recall mode
-offtarget reads in trio mode

1.13.0

Germline changes:

1. polymorphic regions calling improved, working with provided polymorphic regions file
2. one window CNVs detection possible

Somatic changes:

1. Strict quality filters for low clonality variants
2. Filtering of low-quality and polymorphic regions

1.12.0

• Polymorphic regions detection implemented
• Several bug fixes

1.11.0

Methods for segmentation, variance determination changed. Flags --purityStep and --degreesOfFreedomStudent added.