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htslib specifications

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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 https://codeload.github.com/samtools/htslib/tar.gz/1.3.2
Maintained Yes

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https://github.com/samtools/htslib/

htslib citations

 (70)
library_books

Recurrent hotspot mutations in HRAS Q61 and PI3K AKT pathway genes as drivers of breast adenomyoepitheliomas

2018
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 […]

library_books

Detection of functional protein domains by unbiased genome wide forward genetic screening

2018
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). […]

library_books

Adar3 Is Involved in Learning and Memory in Mice

2018
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 (http://www.htslib.org/doc/samtools.html) (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% […]

library_books

Whole genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow

2018
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 (www.htslib.org) 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). […]

call_split

Whole Genome Sequencing of Greater Amberjack (Seriola dumerili) for SNP Identification on Aligned Scaffolds and Genome Structural Variation Analysis Using Parallel Resequencing

2018
PMCID: 5896239
PMID: 29785397
DOI: 10.1155/2018/7984292
call_split See protocol

[…] ). 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 (http://www.htslib.org/download/) and removing pcr duplicates using picard (https://broadinstitute.github.io/picard/). we selected 186,259 nonredundant snps that showed polymorphisms at 10% or more in the 20 […]

library_books

Exome wide somatic mutation characterization of small bowel adenocarcinoma

2018
PMCID: 5871010
PMID: 29522538
DOI: 10.1371/journal.pgen.1007200

[…] []. bamutil v.1.0.13 (http://genome.sph.umich.edu/wiki/bamutil#releases) clipoverlap was used to clip overlapping read pairs. duplicate reads were removed using samtools version 1.0 (http://www.htslib.org/) rmdup on both paired-end and single-end reads []. aligned reads were locally realigned with the genome analysis toolkit (gatk) v.3.5 (https://www.broadinstitute.org/gatk/) indelrealigner […]


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