Atlas2 protocols

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Associated diseases

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Atlas2 specifications

Information


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

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Publications for Atlas2

Atlas2 in pipelines

 (9)
2017
PMCID: 5361813
PMID: 28327206
DOI: 10.1186/s13073-017-0412-6

[…] 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 (http://blog.dnanexus.com/2013-10-22-run-mercury-variant-calling-pipeline/). for research cases, exome […]

2017
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 […]

2016
PMCID: 4965339
PMID: 26820066
DOI: 10.1038/gim.2015.205

[…] 2000., ngs reads were mapped to the hg19 human reference genome using bwa-mem, duplicate reads were removed using picard, local realignments were performed using gatk, and variants were called using atlas2. a population frequency threshold of 0.5% was used to filter out common variants which occur too frequently to be the cause of a rare mendelian disease. four ngs cohort databases were used […]

2016
PMCID: 5007069
PMID: 27602404
DOI: 10.1126/sciadv.1600800

[…] using illumina hiseq 2000. the burrows-wheeler aligner was used to align sequences to the hg19 reference genome (). allele calling and variant call file construction were performed using the atlas2 suite () (atlas-snp and atlas-indel). snvs were excluded if they had a posterior probability <0.95, a total depth of coverage <6×, an allelic fraction <0.1, 99% of reads in a single […]

2016
PMCID: 5088683
PMID: 27799064
DOI: 10.1186/s13073-016-0360-6

[…] of short reads to the human genome reference sequence (grch37) was performed by the burrows-wheeler alignment (bwa) tool. recalibration and variant calling were then performed using gatk [] and the atlas2 suite, respectively []. the mercury pipeline is available in the cloud via dnanexus (http://blog.dnanexus.com/2013-10-22-run-mercury-variant-calling-pipeline/). any individuals or families […]


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Atlas2 in publications

 (51)
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) […]

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 […]

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% […]

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 […]

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 […]


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

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