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@xiao-chen-xc xiao-chen-xc released this 26 Apr 17:37
· 8 commits to main since this release
v3.3.0
16c90e4
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Learn about vigilant mode.

Summary of changes:

  • Improve phasing haplotypes into alleles, allowing (n-1)/1 scenario
  • Do not adjust total_cn from 2 to 4 based on depth when calling fusions
  • Fix rare bugs in depth-related analysis
  • Update ALT alleles to . in the VCF for LowQual calls when ALT is equal to REF
  • Add Ml/Mm tags in Paraphase bam for base modification information
  • In Json output, rename hap_links to haplotype_links and rename linked_haplotypes to raw_alleles
  • For targeted data
    • Improve copy number adjustment based on depth
    • Add option to assume a paralog group to always have more than one copy of gene1
    • Update command line options to use frequency-based parameters: --min-variant-frequency and --min-haplotype-frequency
  • smn1
    • Enable smn1 analysis for CHM13-mapped data (Note that haplogroup assignment is not available with CHM13)
    • Fix bug with assigning haplogroups to smn2 haplotypes
    • Rename smn2_del78 haplotypes to smn_del78
  • hba
    • Do not consider homology haplotypes during allele phasing
    • Better handle hba with targeted data, fixing problems with identifying homology haplotypes
    • Update genotype calls based on phased alleles
    • Report genome coordinates for 3p7 and 4p2 SVs in the sv_called field
  • Minor update to strc and ncf1 for copy number adjustment based on depth
  • Update f8 to reflect SV types in the haplotype name
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