Main tool: clair3
Additional tools installed via micromamba:
Name Version Build Channel
────────────────────────────────────────────────────────────────────────
Jinja2 3.1.6 pypi_0 pypi
MarkupSafe 3.0.2 pypi_0 pypi
_openmp_mutex 4.5 20_gnu conda-forge
amply 0.1.6 pyhd8ed1ab_1 conda-forge
biopython 1.86 py311h49ec1c0_1 conda-forge
boost-cpp 1.85.0 h3c6214e_4 conda-forge
bzip2 1.0.8 hda65f42_9 conda-forge
c-ares 1.34.6 hb03c661_0 conda-forge
ca-certificates 2026.2.25 hbd8a1cb_0 conda-forge
cffi 2.0.0 py311h03d9500_1 conda-forge
coin-or-cbc 2.10.13 h4d16d09_0 conda-forge
coin-or-cgl 0.60.10 hc46dffc_0 conda-forge
coin-or-clp 1.17.11 hc03379b_0 conda-forge
coin-or-osi 0.108.12 hf4fecb4_0 conda-forge
coin-or-utils 2.11.13 hc93afbd_0 conda-forge
docutils 0.22.4 pyhd8ed1ab_0 conda-forge
filelock 3.20.0 pypi_0 pypi
fsspec 2025.12.0 pypi_0 pypi
h5py 3.16.0 pypi_0 pypi
hdf5plugin 6.0.0 pypi_0 pypi
htslib 1.23 h566b1c6_0 bioconda
icu 75.1 he02047a_0 conda-forge
importlib-metadata 8.7.0 pyhe01879c_1 conda-forge
isa-l 2.31.1 hb9d3cd8_1 conda-forge
keyutils 1.6.3 hb9d3cd8_0 conda-forge
krb5 1.22.2 ha1258a1_0 conda-forge
ld_impl_linux-64 2.45.1 default_hbd61a6d_101 conda-forge
libblas 3.11.0 5_h4a7cf45_openblas conda-forge
libboost 1.85.0 h0ccab89_4 conda-forge
libboost-devel 1.85.0 h00ab1b0_4 conda-forge
libboost-headers 1.85.0 ha770c72_4 conda-forge
libcblas 3.11.0 5_h0358290_openblas conda-forge
libcurl 8.19.0 hcf29cc6_0 conda-forge
libdeflate 1.22 hb9d3cd8_0 conda-forge
libedit 3.1.20250104 pl5321h7949ede_0 conda-forge
libev 4.33 hd590300_2 conda-forge
libexpat 2.7.4 hecca717_0 conda-forge
libffi 3.5.2 h3435931_0 conda-forge
libgcc 15.2.0 he0feb66_18 conda-forge
libgcc-ng 15.2.0 h69a702a_18 conda-forge
libgfortran 15.2.0 h69a702a_18 conda-forge
libgfortran5 15.2.0 h68bc16d_18 conda-forge
libgomp 15.2.0 he0feb66_18 conda-forge
liblapack 3.11.0 5_h47877c9_openblas conda-forge
liblapacke 3.11.0 5_h6ae95b6_openblas conda-forge
liblzma 5.8.2 hb03c661_0 conda-forge
liblzma-devel 5.8.2 hb03c661_0 conda-forge
libnghttp2 1.67.0 had1ee68_0 conda-forge
libnsl 2.0.1 hb9d3cd8_1 conda-forge
libopenblas 0.3.30 pthreads_h94d23a6_4 conda-forge
libsqlite 3.52.0 h0c1763c_0 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.2.0 h934c35e_18 conda-forge
libstdcxx-ng 15.2.0 hdf11a46_18 conda-forge
libuuid 2.41.3 h5347b49_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
lightning-utilities 0.15.3 pypi_0 pypi
mpmath 1.3.0 pypi_0 pypi
ncurses 6.5 h2d0b736_3 conda-forge
networkx 3.6.1 pyhcf101f3_0 conda-forge
numexpr 2.14.1 pypi_0 pypi
numpy 2.4.2 py311h2e04523_1 conda-forge
openssl 3.6.1 h35e630c_1 conda-forge
packaging 26.0 pyhcf101f3_0 conda-forge
parallel 20260122 ha770c72_0 conda-forge
pbzip2 1.1.13 h1fcc475_2 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
pigz 2.8 h421ea60_2 conda-forge
pillow 12.0.0 pypi_0 pypi
pip 26.0.1 pyh8b19718_0 conda-forge
pulp 2.8.0 py311h77a8cca_3 conda-forge
pycparser 2.22 pyh29332c3_1 conda-forge
pyfaidx 0.9.0.3 pyhdfd78af_0 bioconda
pyparsing 3.3.2 pyhcf101f3_0 conda-forge
pysam 0.23.3 py311hb456a96_1 bioconda
python 3.11.15 hd63d673_0_cpython conda-forge
python-isal 1.8.0 py311h49ec1c0_1 conda-forge
python-zlib-ng 1.0.0 py311h15805fc_1 conda-forge
python_abi 3.11 8_cp311 conda-forge
pyvcf3 1.0.4 py311haab0aaa_0 bioconda
readline 8.3 h853b02a_0 conda-forge
samtools 1.23 h96c455f_0 bioconda
scipy 1.17.1 py311hbe70eeb_0 conda-forge
setuptools 82.0.1 pyh332efcf_0 conda-forge
six 1.17.0 pyhe01879c_1 conda-forge
sympy 1.14.0 pypi_0 pypi
tk 8.6.13 noxft_h366c992_103 conda-forge
torch 2.10.0+cpu pypi_0 pypi
torchmetrics 1.9.0 pypi_0 pypi
torchvision 0.25.0+cpu pypi_0 pypi
tqdm 4.67.3 pypi_0 pypi
typing_extensions 4.15.0 pypi_0 pypi
tzdata 2025c hc9c84f9_1 conda-forge
uv 0.10.10 pypi_0 pypi
whatshap 2.8 py311he264feb_0 bioconda
wheel 0.46.3 pyhd8ed1ab_0 conda-forge
xopen 2.0.2 pyh707e725_2 conda-forge
xz 5.8.2 ha02ee65_0 conda-forge
xz-gpl-tools 5.8.2 ha02ee65_0 conda-forge
xz-tools 5.8.2 hb03c661_0 conda-forge
zipp 3.23.0 pyhcf101f3_1 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zlib-ng 2.3.3 hceb46e0_1 conda-forge
zstandard 0.25.0 py311haee01d2_1 conda-forge
zstd 1.5.7 hb78ec9c_6 conda-forge
Code repository: https://github.com/HKU-BAL/Clair3
Basic information on how to use this tool:
- executable: run_clair3.sh
- help:
-h,--help - version:
-v,--version - description: A germline small variant caller for long-reads.
Additional information:
- This container includes the following models in
/clair3/modelsand/opt/models - This container has no GPU support!
List of models:
hifi
hifi_revio
hifi_sequel2
ilmn
ont
ont_guppy5
r1041_e82_400bps_hac_v410
r1041_e82_400bps_hac_v500
r1041_e82_400bps_hac_with_mv
r1041_e82_400bps_sup_v410
r1041_e82_400bps_sup_v430_bacteria_finetuned
r1041_e82_400bps_sup_v500
r941_prom_hac_g360+g422
r941_prom_sup_g5014
Full documentation: https://github.com/HKU-BAL/Clair3
run_clair3.sh \
--bam_fn=${BAM} \
--ref_fn=${REF} \
--threads=${THREADS} \
--platform="ont" \ ## options: {ont,hifi,ilmn}
--model_path=${MODEL_PREFIX} \ ## absolute model path prefix
--output=${OUTPUT_DIR} ## absolute output path prefix
## pileup output file: ${OUTPUT_DIR}/pileup.vcf.gz
## full-alignment output file: ${OUTPUT_DIR}/full_alignment.vcf.gz
## Clair3 final output file: ${OUTPUT_DIR}/merge_output.vcf.gz