AlleleSeq protocols

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AlleleSeq specifications


Unique identifier OMICS_05503
Name AlleleSeq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Joel Rozowsky <>

Publication for AlleleSeq

AlleleSeq in pipelines

PMCID: 4512258
PMID: 26140685
DOI: 10.7554/eLife.07860.022

[…] polymorphisms (snps and indels, obtained from the mouse genome project: into the mus musculus grcm38 reference genome sequence using the alleleseq package (). we then mapped each of the cast/eij×c57bl/6j hybrid rna-seq libraries to the splice-junction aware diploid genome using star rna-seq aligner (). for each mapped rna-seq library, […]

PMCID: 4562498
PMID: 26253569
DOI: 10.15252/msb.156240

[…] 2014. the snps and indels between c57bl/6j and spret/eij were downloaded from the sanger institute (; release v3, build 137). the vcf2diploid tool (version 0.2.6) in the alleleseq pipeline was used to construct the spret/eij genome by incorporating the snps and indels into the c57bl/6j genome (rozowsky et al, ). the chain file between the two genomes was also […]

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AlleleSeq in publications

PMCID: 5685192
PMID: 29022598
DOI: 10.1038/nature24265

[…] include only uniquely mapped and properly paired reads contained within exon boundaries., for the four single-cell samples and for gtex-upic rna-seq data was processed using a modification of the alleleseq pipeline, to minimize reference allele bias in alignment. a diploid personal reference genome for each of the samples was generated with the vcf2diploid tool including all heterozygous […]

PMCID: 5514110
PMID: 28717173
DOI: 10.1038/s41598-017-06120-3

[…] analysis., predictsnp and provean were used to predict possible impact of amino acid substitutions/deletions on the structure and function of proteins., the vcf2diploid tool, version 0.2.6a ( was used to reconstruct genotype-specific target genomic., cis-acting regulatory dna elements within the putative regulatory regions of the 34 candidate genes […]

PMCID: 5600873
PMID: 28424518
DOI: 10.1038/nature22074

[…] genome project (pman_1.0, genbank accession: gca_000500345.1). we created a p. polionotus genome and annotation by incorporating snps and indels into the p. maniculatus pman_1.0 reference using the alleleseq package and the ucsc liftover tool. briefly, p. polionotus gdna reads (genbank bioproject accession: prjna53593) were aligned to the pman_1.0 reference using stampy v1.0.21 […]

PMCID: 5886188
PMID: 28335003
DOI: 10.1093/hmg/ddx092

[…] are 20–40% enriched within enhancers but not within promoters (). these patterns of enrichment are reinforced when we stringently select only the most significant vdr-bvs (vdr-sbvs, , fig. s16a; alleleseq fdr ≤ 0.01; 6,715 vdr-bvs) or the 357 recurrent vdr-bvs that are called at the same position in multiple samples (vdr-rbvs, , fig. s16d). we conclude that vdr-bvs are not uniformly […]

PMCID: 5020486
PMID: 27618913
DOI: 10.1186/s12859-016-1238-8

[…] snvs and indels not on the reference panel were assigned randomly to one of the two haplotypes. parental genomes for the simulated individual were generated using the vcf2diploid program within alleleseq [] and parental gtf files were created using the output files and liftover tool. we then mapped the simulated data to both parental genomes using the same mapping tools and filtering […]

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AlleleSeq institution(s)
Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA

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