VarAFT protocols

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

Versioning


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Maintainer


Publication for Variant Annotation and Filter Tool

VarAFT IN pipelines

 (2)
2015
PMCID: 4803780
PMID: 27054082
DOI: 10.1016/j.atg.2015.07.006

[…] of refseq genes was downloaded from ucsc genome browser using table browser option (rosenbloom et al., 2015). 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 […]

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

[…] june 2015) for target regions of 78 genes present in both myopanel1 and myopanel2. this set was then used to calculate coverage of individual mutation positions for each sample using varaft tool. number of mutations with no coverage, less than 6 × coverage and less that 20 × coverage was calculated., we performed a pilot study designed to test and optimize the targeted exome […]

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