Alamut Batch protocols

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Alamut Batch statistics

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Associated diseases

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Alamut Batch specifications

Information


Unique identifier OMICS_05999
Name Alamut Batch
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use License purchase required
Operating system Unix/Linux
License Commercial
Computer skills Advanced
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Versioning


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Alamut Batch in pipelines

 (7)
2017
PMCID: 5384676
PMID: 28388629
DOI: 10.1371/journal.pone.0174264

[…] prior to indel realignment, base quality score recalibration and variant discovery using the genome analysis toolkit (gatk) v.2.3.-4lite., identified variants were annotated using alamut batch standalone v.1.4.4, (database v.2016.03.04) and filtered using the agileexomefilter (http://dna.leeds.ac.uk/agile), essentially as described previously []., a targeting construct […]

2016
PMCID: 4700600
PMID: 26729329
DOI: 10.1186/s12881-015-0265-z

[…] genome analysis toolkit (gatk) v.2.3-4lite []. identified variants were saved in variant call format (vcf) and then annotated with positional, frequency and functional in silico predictions using alamut batch standalone v.1.4.0, (database v.2015.04.30) (interactive biosoftware, rouen, france). these programs included sift (http://sift.jcvi.org), and aligngvgd […]

2016
PMCID: 4754937
PMID: 26880286
DOI: 10.1186/s12881-016-0275-5

[…] genome reference sequence (hg19), duplicate read removal, coverage analysis, and variant calling. variants were annotated with an in-house software package, which makes use of the ensembl api and alamut batch. to reduce the number of variants, synonymous variants with no predicted splice site disruption, variants with an allelic frequency in the global 1000 genomes population >10 % […]

2016
PMCID: 4777533
PMID: 26938746
DOI: 10.1371/journal.pone.0150381

[…] of 50. variants, where two different alleles were observed, were accepted as heterozygote variant calls if the frequency of the minor variant allele was >0.15. variants were analysed using alamut batch (interactive biosoftware, france). mc1r variants were grouped according to potential significance. all missense, non-sense, and frameshift mutations () were assigned to the mc1r variant […]

2016
PMCID: 4819622
PMID: 26733463
DOI: 10.1136/jmedgenet-2015-103620

[…] quality score recalibration and variant discovery, which resulted in variants being saved in variant call format (vcf) before being annotated with positional, functional and frequency data using alamut batch standalone v.1.4.0 (interactive biosoftware, rouen, france). programs ancillary to the automated pipeline were used to interrogate these data, namely agile multiideogram […]


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Alamut Batch in publications

 (18)
PMCID: 5932755
PMID: 29720203
DOI: 10.1186/s13023-018-0812-8

[…] was performed on default settings except for “snp read depth filter”. this value was set to value 10. the aim of this analysis was to increase the sensitivity of the whole process., afterwards, alamut batch (alamut batch 1.5.2, interactive biosoftware, rouen, france) was used for annotating merged vcfs into a tabular file., an alamut batch annotated file in tabular format was used […]

PMCID: 5819082
PMID: 29458332
DOI: 10.1186/s12881-018-0533-9

[…] variant-induced alterations in 3′ and 5′ splice site strength, as described by houdayer et al. 2012 [], except that here both algorithms were interrogated by using the integrated software tool alamut batch version 1.5, (interactive biosoftware, http://www.interactive-biosoftware.com). for prediction of variant-induced impact on exonic splicing regulatory elements (esr), we resorted […]

PMCID: 5769521
PMID: 29371908
DOI: 10.1186/s13053-018-0086-0

[…] to predict variant-induced alterations in 3′ and 5′ splice site strength, as described by houdayer et al. [], except that here both algorithms were interrogated by using the integrated software tool alamut batch version 1.5, (interactive biosoftware, http://www.interactive-biosoftware.com). for prediction of variant-induced impact on exonic splicing regulatory elements (esr), we resorted […]

PMCID: 5581831
PMID: 28900389
DOI: 10.3389/fncel.2017.00263

[…] (analysis of all transcripts), annovar (allele frequency analysis exac, 1000g and esp6500, algorithms the functional significance sift, polyphen2, mutation taster, fatmm, cadd, dann, eigen), and alamut batch (effect on splicing, database dbsnp, clinvar, hgmd professional). raw sequencing data and the mapping results are available upon request., magnetic resonance imaging (mri) study […]

PMCID: 5473876
PMID: 28623346
DOI: 10.1038/s41598-017-02434-4

[…] and coverage analysis were performed with clc genomics workbench v6.0.4 (clc bio). sequencing coverage is summarized in supplementary table . called variants with coverage ≥3 were annotated with alamut batch (interactive biosoftware). only variants with population frequencies less than 10% were considered, according to public databases ncbi dbsnp (http://www.ncbi.nlm.nih.gov/projects/snp/), […]


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