htslib protocols

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htslib statistics

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htslib specifications


Unique identifier OMICS_13459
Name htslib
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
Computer skills Advanced
Version 1.3.1
Stability Stable
Source code URL
Maintained Yes



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Additional information

htslib in pipelines

PMCID: 5805289
PMID: 29420653
DOI: 10.1371/journal.pone.0192446

[…] uniprot gene ontology annotations dataset:, gene ontology tool:, bcftools-1.2.1, online cadd annotation tool:, online vep tool:, we are thankful to dr. qasim ayub, from the wellcome trust […]

PMCID: 5809945
PMID: 29433585
DOI: 10.1186/s13045-018-0563-y

[…] of gene variation calling is shown in additional file : figure s1. single-nucleotide variants (snvs), insertions or deletions (indels), and fusion genes were called using samtools ( and a customized software-novofusion. the mutations were annotated by the annovar ( with information from the cosmic […]

PMCID: 5824822
PMID: 29476136
DOI: 10.1038/s41467-018-02826-8

[…] frequency determination and copy number calling. the analysis was based on the human reference sequence (ncbi build 37) using the following software packages: bwa: 0.7.13, samtools: 1.1 (using htslib 1.1), picard tools: 1.97 (1504), gatk: appistry v2015.1.1–3.4.46–0-ga8e1d99, cnvkit: 0.7.2, pindel: 0.2.5b8, satk: appistry v2015.1.1–1-gea45d62, annovar: v2016feb01, freebayes: 0.9.20, […]

PMCID: 5834213
PMID: 29462190
DOI: 10.1371/journal.ppat.1006881

[…] with parameters—local—qc-filter—score-min c,120,1. draft assemblies were corrected and validated by manual inspection in geneious, version 9.0.4 []. depth of coverage was calculated using samtools (htslib) version 1.2.1 []. remaining (non bornavirus) contigs and non-assembling reads were then taxonomically assessed, first by using the blastn tool to align to the ncbi nucleotide database. […]

PMCID: 5896239
PMID: 29785397
DOI: 10.1155/2018/7984292

[…] ). we detected 7,059,071 mutations in the resequenced data mapped on the reference genome sequence by realigning the regions where mismatches were accumulated using smatools and bcftools ( and removing pcr duplicates using picard ( we selected 186,259 nonredundant snps that showed polymorphisms at 10% or more in the 20 […]

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htslib in publications

PMCID: 5940840
PMID: 29739933
DOI: 10.1038/s41467-018-04128-5

[…] mapping alignment program (tmap, v3.4.1). local realignment was performed using gatk (v3.1.1). putative mutations were interrogated using pileup files generated with samtools mpileup (version 1.2 htslib 1.2.1). mutations present at variant allele frequencies >1% were considered “validated”. mutations that did not validate were excluded from further analyses. given the overall validation […]

PMCID: 5906580
PMID: 29670134
DOI: 10.1038/s41598-018-24400-4

[…] file, and pcr duplicates were marked by using picard tools (picard version 1.128). the quality of the sequencing data post-alignment was assessed by using samtools stats and samtools flagstats (1.1+htslib−1.1), plot-bamstats, bamcheck and plot-bamcheck (fig. )., snvs and small insertions/deletions (indels) were identified using samtools mpileup (v.1.3), followed by bcftools call (v.1.3). […]

PMCID: 5914295
PMID: 29719497
DOI: 10.3389/fnins.2018.00243

[…] (langmead et al., ) to the mouse reference genome (mm10, genome reference consortium grcm38). a-to-g mismatches were called with samtools v1.12 ( (li et al., ). the positions of common snps from dbsnps138 were removed., only positions covered by at least 20 reads with the a-to-g mismatch found on average 5% […]

PMCID: 5884691
PMID: 29632892
DOI: 10.1126/sciadv.aap9873

[…] format., changes in ne for the baleen whales were inferred from genome sequences using the psmc (). we applied psmc v0.6.5-r67 with input files generated using samtools mpileup version 1.2 ( and by applying a minimum mapping and base quality of 30. using vcfutils, minimum and maximum depth of coverage thresholds were set to 0.5 and 2× the sample’s average coverage (table s1). […]

PMCID: 5871010
PMID: 29522538
DOI: 10.1371/journal.pgen.1007200

[…] []. bamutil v.1.0.13 ( clipoverlap was used to clip overlapping read pairs. duplicate reads were removed using samtools version 1.0 ( rmdup on both paired-end and single-end reads []. aligned reads were locally realigned with the genome analysis toolkit (gatk) v.3.5 ( indelrealigner […]

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