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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



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  • person_outline Heng Li <>

Publication for bcftools

bcftools in pipelines

PMCID: 5780301
PMID: 29331171
DOI: 10.1016/j.ymgme.2017.11.003

[…] (1) the sequencing reads were aligned to the human reference genome version hg19 using bowtie 2 , (2) the duplicates were marked and sorted using picard, (3) variants were called using samtools and bcftools after indel realignment using gatk, (4) transcripts were annotated using snpeff , (5) functional variants were prioritized for rare variants by comparison against the public databases […]

PMCID: 5797619
PMID: 29441081
DOI: 10.3389/fpls.2018.00049

[…] sequence in b.g hordei because mapping of b.g. hordei reads on the b.g. tritici reference genome is not possible since the two genomes are highly divergent. the consensus sequences were called using bcftools consensus function after selecting only heterozygous snps and position with a minimum coverage of 10. these sequences were then aligned using muscle (v3.8.31, edgar, ) and maximum likelihood […]

PMCID: 5799372
PMID: 29403008
DOI: 10.1038/s41467-018-02831-x

[…] 2.5 by bowtie2. the resulting data in the sam format were converted to a binary equivalent bam format and sorted using the samtools software package. variant calling was performed with samtools and bcftools., the primers used for pcr are listed in supplementary table . for the complementation analysis of the nrsym1 mutants, a 7.5-kb genomic dna fragment including the nrsym1 candidate gene […]

PMCID: 5808220
PMID: 25741336
DOI: 10.3389/fmicb.2018.00122

[…] samtools idxstats (li, ). redundant reads of the resulted hits were equalized to read/million read. consensus viral sequences from the aligned deduplicated reads were generated using the samtools/bcftools (li and durbin, ) pipeline. coverage of the appropriate genome was counted as % of the genome covered by nucleotide information from the mapped small rna reads. (b) de novo assembling […]

PMCID: 5813019
PMID: 29445215
DOI: 10.1038/s41598-018-21438-2

[…] all publicly available raw illuminatm reads in fastq format for a given taxon. then, it maps the reads onto the desired target loci using bowtie2, and performs variant calling with samtools/bcftools and rematch single nucleotide polymorphism call criteria. the minimum coverage depth to consider a position to be present in the alignment was fixed at 5 reads, and to perform allele calling […]

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bcftools in publications

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

[…] (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 […]

PMCID: 5932867
PMID: 29720102
DOI: 10.1186/s12864-018-4709-7

[…] ratios of alleles at heterozygous sites. samtools was used to process aligned reads [] and heterozygous sites or single nucleotide polymorphisms (snps) were identified from the aligned reads using bcftools []. an average ratio of reads of heterozygous alleles in sliding non-overlapping windows of 10 kb across each scaffold was then used to infer ccnvs []. loss of heterozygosity (loh) was also […]

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

[…] to more than one unique site on the reference genome sequence., 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, […]

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

[…] 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 […]

PMCID: 5920189
PMID: 29700146
DOI: 10.1128/genomeA.00294-18

[…] (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., the complete genome sequences […]

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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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