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SAMBLASTER specifications


Unique identifier OMICS_04682
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format SAM
Output data The discordant read-pairs and/or split-read mappings used for structural variant calling.
Operating system Unix/Linux, Mac OS
Programming languages C++
License MIT License
Computer skills Advanced
Version 0.1.24
Stability Stable
Maintained Yes




No version available


Publication for SAMBLASTER

SAMBLASTER citations


Comprehensive genomic transcriptomic tumor normal gene panel analysis for enhanced precision in patients with lung cancer

PMCID: 5922390
PMID: 29721196
DOI: 10.18632/oncotarget.24973
call_split See protocol

[…] DNA sequencing data was aligned to GRCh37 ( by BWA [], duplicate-marked by samblaster [], and indel realignment and base quality recalibration performed by GATK v2.3 []. RNA sequencing data is aligned by bowtie [] and RNA transcript expression estimated by RSEM []. Tumor vs. […]


Genome sequencing identifies somatic BRAF duplication c.1794_1796dupTAC;p.Thr599dup in pediatric patient with low grade ganglioglioma

PMCID: 5880266
PMID: 29434027
DOI: 10.1101/mcs.a002618

[…] Sequence alignments were refined according to community-accepted guidelines for best practices ( Duplicate sequence reads were removed using samblaster-v.0.1.22, local realignment was performed on the aligned sequence data using the Genome Analysis Toolkit (GATK) (v3.7–0), and Churchill's own deterministic implementation of base quality sc […]


Whole exome sequencing identifies germline mutation in TP53 and ATRX in a child with genomically aberrant AT/RT and her mother with anaplastic astrocytoma

PMCID: 5880256
PMID: 29602769
DOI: 10.1101/mcs.a002246

[…] man reference genome (hg19) using Bowtie2 (version 2.2.5) () and converted to BAM format using SAMtools (version 0.1.19) (). Duplicate reads were marked and removed from the resulting BAM files using SAMBLASTER (version 0.1.21) (). […]


A soft selective sweep during rapid evolution of gentle behaviour in an Africanized honeybee

Nat Commun
PMCID: 5688081
PMID: 29142254
DOI: 10.1038/s41467-017-01800-0

[…] ed reads were aligned to the honeybee reference genome (BeeBase, scaffold assembly of Amel 4.5) with BWA MEM (version 0.7.10) using -M parameter. Aligned/properly mapped reads were de-duplicated with SAMBLASTER (version 0.1.22). De-duplicated samples were then realigned with GATK (version 3.4-0) RealignerTargetCreator followed by IndelRealigner (see Supplementary Note , Step ; Supplementary Data ) […]


Combating subclonal evolution of resistant cancer phenotypes

Nat Commun
PMCID: 5666005
PMID: 29093439
DOI: 10.1038/s41467-017-01174-3
call_split See protocol

[…] his revealed the APC mutation in patient #3 not detected by FreeBayes; all other small variants discussed were identified with FreeBayes.Structural variants were detected from WGS as follows. We used SAMBLASTER v0.1.22 to extract discordant paired-end reads and split reads. LUMPY v0.2.12, or LUMPY within the SpeedSeq suite (sv utility), was used to call structural variants based on these reads, fo […]


Accelerating next generation sequencing data analysis with system level optimizations

Sci Rep
PMCID: 5567265
PMID: 28831090
DOI: 10.1038/s41598-017-09089-1

[…] data and the genome variant discovery. For the genome alignment, we used BWAKIT, which is an open-source tool that includes the pre-compiled ×86_64 binaries of Seqtk, SAMtools, Trimadap, BWA-MEM and Samblaster. Seqtk is a fast and lightweight toolkit for processing sequences in the FASTA/ FASTQ format. Trimadap is used for trimming the adapter sequence from the FASTQ files. The latest version of […]


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SAMBLASTER institution(s)
Department of Biochemistry and Molecular Genetics and Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
SAMBLASTER funding source(s)
Supported by NIH New Innovator Award (DP2OD006493-01) and a Burroughs Wellcome Fund Career Award.


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