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HipSTR v0.4
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@tfwillems tfwillems released this 24 Apr 11:32
· 121 commits to master since this release
v0.4
9202e3a

A lot has changed since the last official release of HipSTR (v0.2). We've extensively improved HipSTR's genotyping accuracy, simplified the tool's usage and added new features. Here's a short synopsis of some of what's changed:

  • We removed the PhasedBEAGLE component of the tool, as it's no longer relevant
  • We removed all dependencies on bamtools and vcflib to simplify compilation
  • HipSTR now uses htslib and wrapper files to read BAM and VCF files
  • HipSTR now supports alignments in CRAM format in addition to BAM format
  • The --use-all-reads option is deprecated, as HipSTR now always uses all reads to boost accuracy
  • A new FORMAT field AB is output to the VCF. This field can be used to filter genotypes with highly biased read counts that are likely genotyping errors
  • The ---min-mapq, --len-genotyper, --hide-allreads, --hide-mallreads, --output-pallreads and --no-pool-seqs options are no longer available
  • de Bruijn graphs are used to assemble sequences flanking the STR region. These sequences are incorporated into the genotyping process, resulting in improved genotyping accuracy
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