Atlas2 protocols

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


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Publications for Atlas2

Atlas2 IN pipelines

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 (17). allele calling and variant call file construction were performed using the atlas2 suite (18) (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 […]

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

[…] 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 [29] and the atlas2 suite, respectively [30]. the mercury pipeline is available in the cloud via dnanexus ( any individuals or families […]

PMCID: 5362362
PMID: 27657687
DOI: 10.1038/gim.2016.131

[…] reads were mapped to a human genome reference sequence (grch37) by the burrows-wheeler alignment (bwa). subsequently, the recalibration was done by gatk,9 and variant calling was performed by the atlas2 suite. 10 the mercury pipeline is available in the cloud via dnanexus (, after detection of all bi-allelic […]

PMCID: 4507324
PMID: 26195989
DOI: 10.1186/s13073-015-0171-1

[…] using casava, mapping of the short reads against a human genome reference sequence (grch37) using the burrows-wheeler alignment (bwa), recalibration using gatk [19], and variant calling using the atlas2 suite [20]. finally, cassandra [21] was used to annotate relevant information about gene names, predicted variant pathogenicity, reference allele frequencies and metadata from external […]

PMCID: 3706849
PMID: 23806086
DOI: 10.1186/gm461

[…] separate sequence-event bams into a single sample-level bam is performed. bam sorting, duplicate read marking, and realignment to improve in/del discovery all occur at this step. next, we used the atlas2 [18] suite (atlas-snp and atlas-indel) to call variants and produce a variant call file (vcf [19]). finally, annotation data is added to the vcf using the cassandra [20] suite of annotation […]

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

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