Version 3.1.1

Summary of changes:
Minor update. Fix program error in low-depth or no-data regions. Completes analysis even when the input is a small bamlet (result is still a no-call).

Version 3.1.0

Summary of changes:

• Improve PMS2/PMS2CL differentiation
• Output protein changes at five potentially pathogenic sites in OPN1LW/OPN1MW
• Update region definitions for some families
• Add a few regions for fusion calling
  • CYP2D6, GBA, CYP11B1, the CFH gene cluster
• Improve VCFs. See documentation here
  • For each region, all gene copies are now in a single VCF file per sample, reported as sample columns in the VCF.
  • Report boundary coordinates and the truncated status of a haplotype in the VCF.
  • Report groups of haplotypes on the same chromosome when this information is available.

Version 3.0.0

Summary of changes:

• Added HBA1/HBA2 and OPN1LW/OPN1MW callers
• Added ~150 segmental duplication regions for GRCh38
• Improved gene callers
  • F8: Improved calling of Intron22 inversion and Exon1-22 deletion
  • NCF1: Improved assignment of genes to NCF1 vs. pseudogenes
  • PMS2: Improved assignment of genes to PMS2 vs. pseudogene. Updated the coordinates of the region to phase
  • IKBKG: Improved assignment of genes to IKBKG vs. pseudogene. Updated the coordinates of the region to phase
  • RCCX: Better calling of a multi-allelic site IVS2-13A/C>G
  • CFC1: Updated the coordinates of the region to phase
• For SMN1/STRC/PMS2/IKBKG/NCF1, variants are now called against the gene for gene haplotypes and against the paralog/pseudogene for paralog/pseudogene haplotypes
• Report F8 Intron 22 inversion and Exon1-22 deletion, and IKBKG 11.7kb deletion in VCFs
• Improved homopolymer/simple repeat masking before phasing
• Included filtered calls in VCFs
• Added GRCh37/hg19 support for 11 medically relevant gene families

Version 2.2.3

• Speeds up single sample analysis through multiprocessing by genomic region (-t is enabled)
• Adds program version and command to BAM and VCF headers
• Fixed a bug that may lead to failed analysis in low coverage samples
• Fixed a bug in F8 analysis

Version 2.2.2

• Fix low depth error so that even if one region fails depth check, the other regions will still produce results.
• Show version

Version 2.2.1

This version includes some light updates to Paraphase

• Simplify config files
• Prevent non-zero exit code
• Minor algorithm improvements

Please note that a new input file is required - the reference genome fasta file (specify with -r)

Version 2.1.0

This release includes some improvements to phasing and variant calling.

• Filter out spurious variants before phasing
• Filter out spurious haplotypes after phasing
• Better handle homozygous cases

Version 2.0.0

This release extends Paraphase to resolve highly homologous genes listed below

• SMN1/SMN2 (spinal muscular atrophy)
• RCCX module
  • CYP21A2 (21-Hydroxylase-Deficient Congenital Adrenal Hyperplasia)
  • TNXB (Ehlers-Danlos syndrome)
  • C4A/C4B (relevant in autoimmune diseases)
• PMS2 (Lynch Syndrome)
• STRC (hereditary hearing loss and deafness)
• IKBKG (Incontinentia Pigmenti)
• NCF1 (chronic granulomatous disease; Williams syndrome)
• NEB (Nemaline myopathy)
• F8 (intron 22 inversion, Hemophilia A)
• CFC1 (heterotaxy syndrome)