Skip to content

v1.4.0
Compare
Choose a tag to compare
@epi2melabs-bot epi2melabs-bot released this 19 Apr 17:15
· 511 commits to master since this release
v1.4.0
d1eb43d

Added

  • --depth_intervals will output a bedGraph file with entries for each genomic interval featuring homogeneous depth
  • --phase_methyl will output haplotype-level methylation calls, using the HP tags added by whatshap in the wf-human-snp workflow
  • --sv_benchmark will benchmark SV calls with Truvari
    • The workflow uses the 'NIST_SVs_Integration_v0.6' truth set and benchmarking should be carried out on HG002 data.

Changed

  • Added coverage barrier to wf-human-variation
  • When the SNP and SV subworkflows are both selected, the workflow will use the results of the SV subworkflow to refine the SNP calls
    • This new behaviour can be disabled with --skip_refine_snp_with_sv
  • Updated to Oxford Nanopore Technologies PLC. Public License
  • Workflow requires target regions to have 20x mean coverage to permit analysis

Fixed

  • report_sv.py now handles empty VCF files
  • report_str.py now handles mono-allelic STR
  • WhatsHap processes do not block for long time with CRAM inputs due to missing REF_PATH
  • filterCalls failure when input BED has more than three columns
  • get_genome assumed STR subworkflow was always enabled, preventing CNV analysis with hg19
  • "genome build (...) is not compatible with this workflow" was incorrectly thrown when the workflow stopped before calling get_genome
Assets 2
Loading