Main Tool: FreeBayes
Code repository: https://github.com/freebayes/freebayes
Basic information on how to use this tool:
- executable:
freebayes - help:
-h,--help - version:
--version - description: FreeBayes is a haplotype-based variant detector and is a great tool for calling variants from a population.
FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. FreeBayes is haplotype-based, in the sense that it calls variants based on the literal sequences of reads aligned to a particular target, not their precise alignment. This model is a straightforward generalization of previous ones (e.g. PolyBayes, samtools, GATK) which detect or report variants based on alignments. This method avoids one of the core problems with alignment-based variant detection — that identical sequences may have multiple possible alignments
Additional tools installed via micromamba:
Name Version Build Channel
───────────────────────────────────────────────────────────────────
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.34.5 hb9d3cd8_0 conda-forge
ca-certificates 2025.7.14 hbd8a1cb_0 conda-forge
fastahack 2016.07.2 h4ac6f70_6 bioconda
freebayes 1.3.10 hbefcdb2_0 bioconda
htslib 1.22.1 h566b1c6_0 bioconda
icu 75.1 he02047a_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
ld_impl_linux-64 2.44 h1423503_1 conda-forge
libasprintf 0.25.1 h8e693c7_0 conda-forge
libcurl 8.14.1 h332b0f4_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 2.7.1 hecca717_0 conda-forge
libffi 3.4.6 h2dba641_1 conda-forge
libgcc 15.1.0 h767d61c_3 conda-forge
libgcc-ng 15.1.0 h69a702a_3 conda-forge
libgettextpo 0.25.1 h5888daf_0 conda-forge
libgomp 15.1.0 h767d61c_3 conda-forge
libidn2 2.3.8 ha4ef2c3_0 conda-forge
liblzma 5.8.1 hb9d3cd8_2 conda-forge
libmpdec 4.0.0 hb9d3cd8_0 conda-forge
libnghttp2 1.64.0 h161d5f1_0 conda-forge
libsqlite 3.50.3 hee844dc_0 conda-forge
libssh2 1.11.1 hcf80075_0 conda-forge
libstdcxx 15.1.0 h8f9b012_3 conda-forge
libstdcxx-ng 15.1.0 h4852527_3 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
ncurses 6.5 h2d0b736_3 conda-forge
openssl 3.5.1 h7b32b05_0 conda-forge
parallel 20250622 ha770c72_0 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
pip 25.1.1 pyh145f28c_0 conda-forge
python 3.13.5 hec9711d_102_cp313 conda-forge
python_abi 3.13 8_cp313 conda-forge
readline 8.2 h8c095d6_2 conda-forge
samtools 1.22.1 h96c455f_0 bioconda
seqlib 1.2.0 hbefcdb2_0 bioconda
tabixpp 1.1.2 hbefcdb2_4 bioconda
tk 8.6.13 noxft_hd72426e_102 conda-forge
tzdata 2025b h78e105d_0 conda-forge
vcflib 1.0.14 h34261f4_0 bioconda
wget 1.21.4 hda4d442_0 conda-forge
zlib 1.3.1 hb9d3cd8_2 conda-forge
zstd 1.5.7 hb8e6e7a_2 conda-forge
Full documentation: Garrison, E., & Marth, G. (2012). Haplotype-based variant detection from short-read sequencing. ArXiv.org.
# basic usage
freebayes -f [REFERENCE] [OPTIONS] [BAM FILES] > [OUTPUT]
# example
freebayes --bam Sample_1_sorted.bam --ploidy 1 --fasta-reference reference.fasta --vcf Sample1_freebayes.vcf