Clair3 Versions Save

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

v1.0.8

1 month ago
  1. Fixed an issue in VCF output that caused occasional quality score small differences compared to GVCF output.
  2. Updated LongPhase to version 1.7.

v1.0.7

1 month ago
  1. Added memory guards and test functions to the full-alignment calling C implementation (#286 by @Chris Wright).
  2. Increased the maximum mpileup read coverage to 2^20 to accomodate excessively high-coverage amplicon data (#292 by @Devon Ryan).
  3. Updated LongPhase to version 1.6.

v1.0.6

2 months ago
  1. Fixed stack overflow issue when the read coverage is excessively high (#282 by @Chris Wright, #265 by @ymcki).
  2. Added reference caching for CRAM input (#278 by @Alex Leonard, #180 by @bartcharbon and @SamStudio8).
  3. Fixed a bug that outputs RefCall calls when no variant is called by full-alignment model (#271).
  4. Fixed a bug that variants below min coverage were still being called (#262).
  5. Set --min_snp_af and --min_indel_af to 0.0 when --vcf_fn is provided (https://github.com/HKU-BAL/Clair3/issues/261).

v1.0.5

5 months ago
  1. Fixed the issue showing wrong multi-allelic AF when read coverage is excessively high (#241).
  2. Added --base_err and --gq_bin_size options that can resolve the problem of having excessive GT ./. in GVCF output (#220).
  3. Modified logs (#231, #225)

v1.0.4

10 months ago
  1. Added showing command line and reference source in output VCF header.
  2. Fixed a bug in showing the AF tag for 1/2 genotypes.
  3. Added AD tag output.

v1.0.3

11 months ago

Fixed a bug when the contig name contains colons (#203)

v1.0.2

1 year ago
  1. Added PacBio HiFi Revio model, check Pre-trained model for model usage.
  2. Fixed a bug that halts the pipeline when there exists too few variant candidates (https://github.com/HKU-BAL/Clair3/issues/198).

v1.0.1

1 year ago
  1. Bumped up "WhatsHap" version to 1.7, the whatshap haplotag step is ~15% faster. (#193).
  2. Fixed PL tag output error when ALT is N (#191, contributor @Dennis Hendriksen).

v1.0.0

1 year ago
  1. Added Clair3 version number to the VCF header (#141).
  2. Fixed the numpy.int issue when using newer numpy version (#165, PR contributor @Aaron Tyler).
  3. The new version converts all IUPAC bases to 'N' in both VCF and GVCF output, use --keep_iupac_bases to keep the IUPAC bases (#153).
  4. Added options --use_longphase_for_intermediate_phasing, --use_whatshap_for_final_output_phasing, --use_longphase_for_final_output_phasing, --use_whatshap_for_final_output_haplotagging to disambiguate intermediate phasing and final VCF phasing either using WhatsHap or LongPhase, old options are still usable (#164).
  5. Fixed "shell script interpreter selection problem" when using Clair3 as a host user within a Docker container (#175).

v0.1-r12

1 year ago
  1. CRAM input is supported (https://github.com/HKU-BAL/Clair3/issues/117).
  2. Bumped up dependencies' version to "Python 3.9" (https://github.com/HKU-BAL/Clair3/issues/96), "TensorFlow 2.8", "Samtools 1.15.1", "WhatsHap 1.4".
  3. VCF DP tag now shows raw coverage for both pileup and full-alignment calls (before r12, sub-sampled coverage was shown for pileup calls if average DP > 144, (https://github.com/HKU-BAL/Clair3/issues/128).
  4. Fixed Illumina representation unification out-of-range error in training (https://github.com/HKU-BAL/Clair3/issues/110).