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bcftools specifications


Unique identifier OMICS_13458
Name bcftools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BCF, VCF, BAM
Output format BCF, VCF, BAM
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, Perl
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.3.1
Stability Stable
Source code URL https://codeload.github.com/samtools/bcftools/tar.gz/1.3.1
Maintained Yes




No version available



  • person_outline Heng Li

Publication for bcftools

bcftools citations


Genomic features of renal cell carcinoma with venous tumor thrombus

Sci Rep
PMCID: 5945671
PMID: 29748622
DOI: 10.1038/s41598-018-25544-z

[…] st (9)) (both part of the biobambam package version 0.0.148).The generated bam files were used to identify high-confidence somatic SNVs by applying an in-house analysis pipeline based on samtools and bcftools (both version 0.1.19) as described earlier,. Briefly, samtools version 0.1.19 was used for calling all candidate variants (positions where the tumor sample differs from the reference sequence […]


Environmental fluctuations accelerate molecular evolution of thermal tolerance in a marine diatom

Nat Commun
PMCID: 5928086
PMID: 29712900
DOI: 10.1038/s41467-018-03906-5

[…] We identified candidate SNVs in BWA-mem alignments of genomic sequence reads against the reference genome sequence using the SAMtools/BCFtools pipeline version 1.3.1. Candidate SNVs were identified using bcftools 1.3.1 with the following command-lines:“samtools mpileup -u -f genome.fasta alignment.bam >alignment.bcf” and“bcftools ca […]


Ginkgo biloba’s footprint of dynamic Pleistocene history dates back only 390,000 years ago

BMC Genomics
PMCID: 5921299
PMID: 29703145
DOI: 10.1186/s12864-018-4673-2

[…] wa version 0.7.5a []. After quality filtering and deduplication with samtools version 1.6 [], variants where called using freebayes version 1.1.0-50 [] and consensus sequences extracted as FASTA with bcftools version 1.6 []. The resulting sequences where aligned using Clustal Omega [], the alignment was checked and trimmed in PhyDE version 0.9971 []. Calculations were done using DNASp version 6.10 […]


Whole Genome Sequences of 18 Bovine Alphaherpesvirus 1 Field Isolates from Pennsylvania and Minnesota

Genome Announc
PMCID: 5920189
PMID: 29700146
DOI: 10.1128/genomeA.00294-18
call_split See protocol

[…] .1 (GenBank accession number JX898220) using the bwa-mem algorithm (). Variants were called using freebayes (). Low-quality variants were filtered out, and consensus sequences were obtained using the bcftools consensus tool (http://github.com/samtools/bcftools). Based on phylogenetic analysis, the isolates were all identified as belonging to the BHV1.1 genotype. […]


Ancient DNA from latrines in Northern Europe and the Middle East (500 BC–1700 AD) reveals past parasites and diet

PLoS One
PMCID: 5918799
PMID: 29694397
DOI: 10.1371/journal.pone.0195481

[…] 1.2 []. Alignment coverage and depths were calculated using Paleomix version 1.1.1, commands coverage and depths []. Mitochondrial consensus sequences were called using the commands samtools mpileup, bcftools call (version 1.2) and vcfutils vcf2fq.The consensus sequences from T. trichiura and T. muris were aligned together with all mitochondrial genome sequence of Trichuris genera publicly availab […]


Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene evolution in the Viannia subgenus

R Soc Open Sci
PMCID: 5936940
PMID: 29765675
DOI: 10.1098/rsos.172212

[…] The filtered reads with Smalt as mapped above were used for calling SNPs using Samtools Pileup v0.1.11 and Mpileup v0.1.18 and quality-filtered with Vcftools v0.1.12b and Bcftools v0.1.17-dev as previously [] such that SNPs called by both Pileup and Mpileup post-screening were considered valid. These SNPs all had: base quality greater than 25; mapping quality greater t […]

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bcftools institution(s)
Medical Population Genetics Program, Broad Institute, Cambridge, MA, USA
bcftools funding source(s)
This work was suppported by the National Institutes of Health (1U01HG005208-01).

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