VarAFT protocols

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VarAFT statistics

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Associated diseases

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VarAFT specifications

Information


Unique identifier OMICS_15743
Name VarAFT
Alternative name Variant Annotation and Filter Tool
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format BAM, VCF
Output format BAM, VCF, TXT
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 2.06
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

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Publication for Variant Annotation and Filter Tool

VarAFT in pipelines

 (2)
2016
PMCID: 4931670
PMID: 27120622
DOI: 10.3390/cells5020021

[…] were computed using the bedtools suite v2.17 [] and in-house scripts. variants were identified using the torrent browser variant caller (version 4.0.2), annotated and prioritized with the in-house “varaft” system that includes annovar []., fibroblasts were grown on coverslips (lab-tek, spl life sciences) after 30 nm small interference rna (sirna) treatment for 48 h and fixed in 4% paf solution […]

2015
PMCID: 4803780
PMID: 27054082
DOI: 10.1016/j.atg.2015.07.006

[…] all the splice variants of refseq genes was downloaded from ucsc genome browser using table browser option (). coverage and depth statistics for this set of exons were obtained for each sample using varaft tool. sample p54 was excluded from the analysis due to much lower quality of sequencing results obtained., a set of 11,467 published mutations was obtained from locus specific mutation […]


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VarAFT in publications

 (2)
PMCID: 5622860
PMID: 28751561
DOI: 10.3324/haematol.2016.160192

[…] (illumina) (integragen), as well as another pipeline based on bwa-mem, sambamba, and gatk (inserm umr s910, marseille, france). merge analysis, data mining and manual review were performed using varaft (http://varaft.eu) and alamut software (interactive biosoftware, rouen, france). to investigate genomic copy number aberrations (e.g., copy number gains and copy number losses), we used […]

PMCID: 4803780
PMID: 27054082
DOI: 10.1016/j.atg.2015.07.006

[…] regions using ffpe option in suredesign and added to the total number of probes designed with the default parameters., coverage of the target exons was obtained for each sample with the help of varaft tool (http://varaft.eu, june 2015), which uses bedtools () to compute coverage statistics. for each exon, we verified whether it was 100% covered at 5 × in at least eight out of ten samples. […]


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