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Atlas2 specifications


Unique identifier OMICS_00051
Name Atlas2
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input data Sequence alignment data, reference genome data
Input format BAM, FASTA
Output data Variant calls
Output format VCF
Operating system Unix/Linux
Parallelization MapReduce
Computer skills Advanced
Version 1.4.3
Stability Stable
High performance computing Yes
Maintained Yes


  • Atlas-indel
  • Atlas-SNP


No version available

Publications for Atlas2

Atlas2 citations


Whole exome sequencing in 342 congenital cardiac left sided lesion cases reveals extensive genetic heterogeneity and complex inheritance patterns

Genome Med
PMCID: 5664429
PMID: 29089047
DOI: 10.1186/s13073-017-0482-5
call_split See protocol

[…] erage at shared sites). In both cohorts, read mapping to Genome Reference Consortium Human Build 37 (GRCh37) was performed with Burrows-Wheeler alignment [], and allele calling was performed with the Atlas2 suite (Atlas-SNP, Atlas-Indel) []. The Variant Call Format (VCF) file contained flagged low-quality variants including SNPs with posterior probability lower than 0.95, total depth of coverage l […]


Comprehensive benchmarking of SNV callers for highly admixed tumor data

PLoS One
PMCID: 5636151
PMID: 29020110
DOI: 10.1371/journal.pone.0186175

[…] ree callers had sensitivity and precision above 90% and 99% on exome data, respectively, and even higher average sensitivities on panel data for similar precision (98%, 99%; ). Evaluation results for Atlas2 on exome data are missing as the experiments were not finished successfully. The worst performance on exome data was seen for VarScan2 (89.3% sensitivity). The best callers for exome data were […]


Unraveling genetic predisposition to familial or early onset gastric cancer using germline whole exome sequencing

Eur J Hum Genet
PMCID: 5643972
PMID: 28875981
DOI: 10.1038/ejhg.2017.138
call_split See protocol

[…] 0 platform (Illumina, Inc.). Subsequently, reads were mapped and aligned to the Human Genome Reference Assembly GRCh37/hg19 using the BCM-HGSC Mercury pipeline. Variant calling was performed with the Atlas2 and SAMtools algorithms; variant annotation was performed with an in-house developed annotation pipeline based on ANNOVAR. Custom scripts were used incorporating multiple databases to retrieve […]


Whole exome sequence based association analyses of plasma amyloid β in African and European Americans; the Atherosclerosis Risk in Communities Neurocognitive Study

PLoS One
PMCID: 5509141
PMID: 28704393
DOI: 10.1371/journal.pone.0180046
call_split See protocol

[…] y Alignment/Map (BAM) files. Aligned reads were then recalibrated using the Genome Analysis ToolKit [], BAM sorting, duplicate read marking, and realignment near insertions or deletions (indels). The Atlas2 [] suite called both single nucleotide variants (SNVs) and indels, generating high-quality variant call files.The ARIC exome sequence was quality controlled as part of the Cohorts for Hearts an […]


Lessons learned from additional research analyses of unsolved clinical exome cases

Genome Med
PMCID: 5361813
PMID: 28327206
DOI: 10.1186/s13073-017-0412-6

[…] rrows-Wheeler Alignment (BWA) tool was utilized to map short reads to the human genome reference sequence (GRCh37). Finally, the recalibration and variant calling were performed using GATK [] and the Atlas2 suite, respectively []. The Mercury pipeline is available in the cloud via DNANexus ( For research cases, exome varian […]


An exome sequencing study of Moebius syndrome including atypical cases reveals an individual with CFEOM3A and a TUBB3 mutation

PMCID: 5334472
PMID: 28299356
DOI: 10.1101/mcs.a000984
call_split See protocol

[…] GSC in-house developed Mercury pipeline () (, achieving an average coverage of 116× read depth (Supplemental Table 1). Variant calling was performed using the Atlas2 () and SAMtools () algorithms. Variants were annotated using intramurally developed pipelines for their coding potential (exonic, intronic, or intragenic) and anticipated functional effects (sy […]


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Atlas2 institution(s)
The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA

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