(in a whisper) bcftools
the world is burning and I'm just sitting here trying to do my job updating some variant calling teaching material and my god the absolute state of the gatk documentation.
February 6, 2025 at 12:03 AM
(in a whisper) bcftools
Release 1.22 of HTSlib, SAMtools, and BCFtools is now available from GitHub. See htslib.org/download/ for links to tarballs and release notes. 🧪
#samtools #bcftools #htslib #bioinformatics
#samtools #bcftools #htslib #bioinformatics
Samtools
Samtools
htslib.org
May 30, 2025 at 10:22 AM
Release 1.22 of HTSlib, SAMtools, and BCFtools is now available from GitHub. See htslib.org/download/ for links to tarballs and release notes. 🧪
#samtools #bcftools #htslib #bioinformatics
#samtools #bcftools #htslib #bioinformatics
From @ksamuk.bsky.social 's thread:
You can restore the old explicit missingness using bcftools: bcftools +setGT your.vcf.gz -- -t q -n . -e 'FMT/DP>=1'
You can restore the old explicit missingness using bcftools: bcftools +setGT your.vcf.gz -- -t q -n . -e 'FMT/DP>=1'
February 7, 2024 at 8:14 PM
From @ksamuk.bsky.social 's thread:
You can restore the old explicit missingness using bcftools: bcftools +setGT your.vcf.gz -- -t q -n . -e 'FMT/DP>=1'
You can restore the old explicit missingness using bcftools: bcftools +setGT your.vcf.gz -- -t q -n . -e 'FMT/DP>=1'
BCFtools/liftover: bcftools plugin to convert genetic variants across genome assemblies academic.oup.com/bioinformati... 🧬🖥️ github.com/freeseek/sco...
January 23, 2024 at 10:59 AM
BCFtools/liftover: bcftools plugin to convert genetic variants across genome assemblies academic.oup.com/bioinformati... 🧬🖥️ github.com/freeseek/sco...
Oh great, thank you google, I had no idea this completely undocumented feature existed in bcftools. I will definitely try this.
June 3, 2025 at 1:37 PM
Oh great, thank you google, I had no idea this completely undocumented feature existed in bcftools. I will definitely try this.
SAMtools / HTSLib / BCFTools 1.23 has been released. See the releasenotes on GitHub and www.htslib.org for details.
Samtools
Samtools
www.htslib.org
December 16, 2025 at 3:33 PM
SAMtools / HTSLib / BCFTools 1.23 has been released. See the releasenotes on GitHub and www.htslib.org for details.
Important comparison of Bcftools and GTK in simulated Drosophila genomes: "by benchmark analyses with a simulated insect population...Bcftools mpileup performs better than GATK HaplotypeCaller in terms of recovery rate and accuracy regardless of mapping software."
The evaluation of Bcftools mpileup and GATK HaplotypeCaller for variant calling in non-human species...
Scientific Reports - The evaluation of Bcftools mpileup and GATK HaplotypeCaller for variant calling in non-human species
www.nature.com
October 10, 2023 at 7:35 PM
Important comparison of Bcftools and GTK in simulated Drosophila genomes: "by benchmark analyses with a simulated insect population...Bcftools mpileup performs better than GATK HaplotypeCaller in terms of recovery rate and accuracy regardless of mapping software."
Release 1.24 of HTSlib, SAMtools, and BCFtools is now available from GitHub. See htslib.org/download/ for links to tarballs and release notes.
🧪🧬🖥️
🧪🧬🖥️
Samtools
Samtools
htslib.org
July 9, 2026 at 3:13 PM
Release 1.24 of HTSlib, SAMtools, and BCFtools is now available from GitHub. See htslib.org/download/ for links to tarballs and release notes.
🧪🧬🖥️
🧪🧬🖥️
Comp-bio hive mind needed! A friend of mine discovered some odd behavior of the -C ("adjust MQ") parameter in bcftools mpileup and wrote about it here: github.com/samtools/bcf...
If anyone has come across / dealt with this before, we'd very much appreciate feedback!
If anyone has come across / dealt with this before, we'd very much appreciate feedback!
How does mpileup adjust-MQ actually work? · Issue #2217 · samtools/bcftools
Hi there, first of all, thanks for making bcftools! It's really amazing to have these kind of tools available. I find the documentation around the mpileup option --adjust-MQ a bit lacking though an...
github.com
July 26, 2024 at 7:30 AM
Comp-bio hive mind needed! A friend of mine discovered some odd behavior of the -C ("adjust MQ") parameter in bcftools mpileup and wrote about it here: github.com/samtools/bcf...
If anyone has come across / dealt with this before, we'd very much appreciate feedback!
If anyone has come across / dealt with this before, we'd very much appreciate feedback!
Today's pysam 0.24.0 release bundles htslib, samtools, and bcftools 1.23.1 and has pre-built wheels for Python 3.8 through 3.14. Notably it includes modified_bases fixes thanks to reports by Leszek Pryszcz and Jun Mencius, and new documentation for VariantRecord et al written by @timd.one. 🧬🖥️
Release v0.24.0 · pysam-developers/pysam
This pysam release wraps htslib/samtools/bcftools version 1.23.1 (PR #1343, PR #1372, and PR #1396) and now requires Cython 3.
It has been tested with Python versions 3.8 through 3.14, and wheels a...
github.com
April 27, 2026 at 12:31 PM
Today's pysam 0.24.0 release bundles htslib, samtools, and bcftools 1.23.1 and has pre-built wheels for Python 3.8 through 3.14. Notably it includes modified_bases fixes thanks to reports by Leszek Pryszcz and Jun Mencius, and new documentation for VariantRecord et al written by @timd.one. 🧬🖥️
QuickVariants 🦠🧬🧪- a genetic variant identification tool developed for microbes, now on Bioconda! 🚀
• 9× faster median speed vs bcftools
• Higher accuracy for both SNPs & indels
bioconda.github.io/recipes/quic...
bmcbiol.biomedcentral.com/articles/10....
#microsky #microbiomesky
• 9× faster median speed vs bcftools
• Higher accuracy for both SNPs & indels
bioconda.github.io/recipes/quic...
bmcbiol.biomedcentral.com/articles/10....
#microsky #microbiomesky
Fast and accurate variant identification tool for sequencing-based studies - BMC Biology
Background Accurate identification of genetic variants, such as point mutations and insertions/deletions (indels), is crucial for various genetic studies into epidemic tracking, population genetics, a...
bmcbiol.biomedcentral.com
September 18, 2025 at 10:02 AM
QuickVariants 🦠🧬🧪- a genetic variant identification tool developed for microbes, now on Bioconda! 🚀
• 9× faster median speed vs bcftools
• Higher accuracy for both SNPs & indels
bioconda.github.io/recipes/quic...
bmcbiol.biomedcentral.com/articles/10....
#microsky #microbiomesky
• 9× faster median speed vs bcftools
• Higher accuracy for both SNPs & indels
bioconda.github.io/recipes/quic...
bmcbiol.biomedcentral.com/articles/10....
#microsky #microbiomesky
depois do R agora é a vez do bcftools fazer um JOGO comigo
October 14, 2025 at 7:38 PM
depois do R agora é a vez do bcftools fazer um JOGO comigo
Release 1.22 of HTSlib, SAMtools, and BCFtools is now available from GitHub. See htslib.org/download/ for links to tarballs and release notes.
Samtools
Samtools
htslib.org
May 31, 2025 at 7:49 AM
Release 1.22 of HTSlib, SAMtools, and BCFtools is now available from GitHub. See htslib.org/download/ for links to tarballs and release notes.
Authors published a paper in Biorxiv, they used SAMtools/BCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #OpenScience
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #OpenScience
www.biorxiv.org
September 23, 2026 at 12:00 PM
Authors published a paper in Biorxiv, they used SAMtools/BCFtools in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #OpenScience
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #methodsmatter #OpenScience
Wanting to share our new preprint relevant to the #consgen community! Want to measure runs of homozygosity but don’t have enough depth for Plink or BCFtools? We show that it can be done as low as ~3-5X in ROHan but careful parameterization and interpretation is key: www.authorea.com/users/857111...
Accurate runs of homozygosity estimation from low coverage genome sequences in non-model species
Runs of homozygosity (ROH) are increasingly being analyzed using whole genome sequences in non-model species as a measure of inbreeding and to assess demographic history, thus providing useful informa...
www.authorea.com
November 18, 2024 at 5:38 PM
Wanting to share our new preprint relevant to the #consgen community! Want to measure runs of homozygosity but don’t have enough depth for Plink or BCFtools? We show that it can be done as low as ~3-5X in ROHan but careful parameterization and interpretation is key: www.authorea.com/users/857111...
Note with the new release (1.24) of samtools / bcftools / htslib, we took the decision to drop CRAM 4.0 support. This is because htslib was the only thing that implemented it AFAIK, it was an experimental prerelease and not an adopted standard, and sadly it wasn't as well engineered as it should be
July 9, 2026 at 3:21 PM
Note with the new release (1.24) of samtools / bcftools / htslib, we took the decision to drop CRAM 4.0 support. This is because htslib was the only thing that implemented it AFAIK, it was an experimental prerelease and not an adopted standard, and sadly it wasn't as well engineered as it should be
Working with Ultima data ATM and using bwa + bcftools. Bcftools has a preset for calling w Ultima. Quality comparable to Illumina although the techn. apparently behaves differently across homopolymers (if I remember correctly, worse). Seems to give good data even after stringent hard filters though
August 16, 2026 at 8:30 PM
Working with Ultima data ATM and using bwa + bcftools. Bcftools has a preset for calling w Ultima. Quality comparable to Illumina although the techn. apparently behaves differently across homopolymers (if I remember correctly, worse). Seems to give good data even after stringent hard filters though
I've done WGS with AVITI and NovaSeq for the same kind of samples, exact same pipeline works fine. FASTP, then MetaHit assembly or BWA-MEM alignment > bcftools mpileup for variant calling
August 16, 2026 at 4:08 PM
I've done WGS with AVITI and NovaSeq for the same kind of samples, exact same pipeline works fine. FASTP, then MetaHit assembly or BWA-MEM alignment > bcftools mpileup for variant calling
bcftools，奥が深いというか頑固というか，使用者の愚かさを深く認識させてくるタイプのツールだ…。うまくいかないときに彼が悪いことは絶対になく，必ずぼくが悪い。
July 8, 2026 at 6:59 AM
bcftools，奥が深いというか頑固というか，使用者の愚かさを深く認識させてくるタイプのツールだ…。うまくいかないときに彼が悪いことは絶対になく，必ずぼくが悪い。
Unfortunately, Lv et al. includes several early sequences riddled with informatics errors. These errors were highlighted in Pekar 2022 - long-known bug in bcftools.
Re. C29095T, that residue flipped repeatedly throughout the early (and later) pandemic, so there's no meaningful signal to grab onto.
Re. C29095T, that residue flipped repeatedly throughout the early (and later) pandemic, so there's no meaningful signal to grab onto.
August 23, 2024 at 6:43 PM
Unfortunately, Lv et al. includes several early sequences riddled with informatics errors. These errors were highlighted in Pekar 2022 - long-known bug in bcftools.
Re. C29095T, that residue flipped repeatedly throughout the early (and later) pandemic, so there's no meaningful signal to grab onto.
Re. C29095T, that residue flipped repeatedly throughout the early (and later) pandemic, so there's no meaningful signal to grab onto.
New Samtools, Htslib and Bcftools 1.19 releases available.
github.com/samtools/sam... and co.
#bioinformatics 🧪
github.com/samtools/sam... and co.
#bioinformatics 🧪
December 12, 2023 at 4:22 PM
New Samtools, Htslib and Bcftools 1.19 releases available.
github.com/samtools/sam... and co.
#bioinformatics 🧪
github.com/samtools/sam... and co.
#bioinformatics 🧪
The htslib.org web site for samtools/htslib/bcftools, or generally get source code from the respective (mostly) GitHub repositories. Build binaries yourself or get them from relatively trusted sources like Linux distributions, brew, or bioconda.
Samtools
Samtools
htslib.org
September 15, 2025 at 12:24 PM
The htslib.org web site for samtools/htslib/bcftools, or generally get source code from the respective (mostly) GitHub repositories. Build binaries yourself or get them from relatively trusted sources like Linux distributions, brew, or bioconda.
Release 1.23.1 of HTSlib, SAMtools, and BCFtools is now available from GitHub. This fixes crashes that could occur when reading malformed CRAM or GZI files. See htslib.org/download/ for links to tarballs and release notes.
🧪🧬🖥️
#samtools #bioinformatics #genomics
🧪🧬🖥️
#samtools #bioinformatics #genomics
Samtools
Samtools
htslib.org
March 18, 2026 at 5:16 PM
Release 1.23.1 of HTSlib, SAMtools, and BCFtools is now available from GitHub. This fixes crashes that could occur when reading malformed CRAM or GZI files. See htslib.org/download/ for links to tarballs and release notes.
🧪🧬🖥️
#samtools #bioinformatics #genomics
🧪🧬🖥️
#samtools #bioinformatics #genomics