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Published March 21, 2025 | Version v1.0.11
Software Open

HKU-BAL/Clair3: v1.0.11

Creators

  • 1. The University of Hong Kong
  • 2. Department of Computer Science, The University of Hong Kong
  • 3. Oxford Nanopore Technologies
  • 4. @nanoporetech, @epi2me-labs
  • 5. Rancho Biosciences
  • 6. ETHZ

Description

  1. Added the --enable_variant_calling_at_sequence_head_and_tail option to enable variant calling at the head and tail 16bp of each sequence. Use with caution because alignments are less reliable in the regions, and there would be insufficient context to be fed to the neural network for reliable calling (#257 by @0peterk87 and multiple contributors).
  2. Added --output_all_contigs_in_gvcf_header to show all contigs IDs in the GVCF header (#371 by @alexnater), regardless whether a contig is covered at least a read or not.
  3. Added a postprocessing script named AddPairEndAlleleDepth to add the "PEAD" tag for showing short-read pair-end allele depth (by Dr. Bin Guan from NEI).
  4. Fixed AF value format issue in GVCF output that caused problem running bcftools merge (#365 by @jimmykhchiu). 5. Added a workflow to split reads into haplotypes according to phased variants and the do variant calling on single haplotypes. More details are in here.
  5. Added set -o pipefail to run_clair3.sh so the non-zero returns of any part of the pipeline is now returned on failure (#368 by @Shians).
  6. . Updated parameter descriptions for clarity (#369 by @Shians).

Files

HKU-BAL/Clair3-v1.0.11.zip

Files (1.0 MB)

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Additional details

Related works

Is supplement to
Software: https://github.com/HKU-BAL/Clair3/tree/v1.0.11 (URL)

Software

Repository URL
https://github.com/HKU-BAL/Clair3