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HipSTR v0.5
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@tfwillems tfwillems released this 05 Aug 21:14
· 85 commits to master since this release
v0.5
bd58649

The latest version of HipSTR contains a handful of minor bug fixes but mainly focuses on adding functionality that makes the tool more robust and easier to run. Here's a summary of the changes in the latest release:

  • Added an FS FORMAT field to the VCF. This field can be used to detect genotyping errors when strand bias is unusually high
  • Added --quiet and --silent command line options that can be used to control the level of detail in the log
  • Rigorously check that all input files (STR region BED, BAM/CRAMs and SNP VCFs) are consistent in terms of contig names
  • Resolved a handful of python3 incompatibilities in the VizAln and VizAlnPDF scripts and they now work with both python2/python3
  • All contigs in the input FASTA file are now written to the VCF header. This prevents downstream errors when validating HipSTR's VCFs using Picard/GATK
  • Added command line options --max-hap-flanks and --min-flank-freq to control the candidate haplotype sequences that flank the STR that are considered during genotyping
  • Automatically filter low frequency flanking haplotype sequences (freq <1%) to improve runtime and reduce memory usage and
  • Added a --output-filters command line option that adds a FILTER FORMAT field to the VCF. For samples with missing genotypes, it describes why the sample was skipped, while for other samples it merely contains PASS
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