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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


Genetic identification and molecular modeling characterization reveal a novel PROM1 mutation in Stargardt4 like macular dystrophy

PMCID: 5787432
PMID: 29416601
DOI: 10.18632/oncotarget.22343

[…] recalibration and local realignment were analyzed using the genome analysis toolkit (gatk version 1.0.5974), and the refined sequencing results were subjected to variant calling using a toolkit (atlas2). variant annotation was performed by applying annovar. sequencing depth > 4, the estimated copy number ≤ 2, snp quality > 20 (score 20 represents 99% accuracy of a base call) […]


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

[…] 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 […]


Exome Wide Meta Analysis Identifies Rare 3′ UTR Variant in ERCC1/CD3EAP Associated with Symptoms of Sleep Apnea

Front Genet
PMCID: 5651235
PMID: 29093733
DOI: 10.3389/fgene.2017.00151

[…] were recalibrated using gatk (depristo et al., ) together with bam sorting, duplicate read marking, and realignment near insertions or deletions. snvs, insertions and deletions were called using atlas2 (challis et al., ). snvs were excluded with low snv posterior probability (<0.95), low variant read count (<3), variant read ratio <0.25 or >0.75, strand-bias of more than 99% […]


Comprehensive benchmarking of SNV callers for highly admixed tumor data

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

[…] 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 […]


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

[…] 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 […]


Evolution of Alu Subfamily Structure in the Saimiri Lineage of New World Monkeys

Genome Biol Evol
PMCID: 5622375
PMID: 28957461
DOI: 10.1093/gbe/evx172

[…] once the data was imported, label names were created for each node and sizes were entered to reflect the subfamily size indicated by coseg. the layouts used were fruchterman reingold and force atlas2 (prevent overlap and scaling was changed to 50). under “appearance”, node size and edge/branch size was adjusted to reflect the numbers entered for size and weight., next, a custom […]

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

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