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URL: http://www.ccmb.med.umich.edu/ccdu/SNPAAMapper
Proper Citation: SNPAAMapper (RRID:SCR_002012)
Description: A downstream variant annotation program that can effectively classify variants by region (e.g. exon, intron, etc), predict amino acid change type (e.g. synonymous, non-synonymous mutation, etc), and prioritize mutation effects (e.g. CDS versus 5?UTR, etc). Major features: * The pipeline accepts the VCF (Variant Call Format) input file in tab-delimited format and processes the vcf input file containing all cases (G5, lowFreq, and novel) * The variant mapping step has the option of letting users select whether they want to report the bp distance between each identified intron variant and its nearby exon * The pipeline can deal with VCF files called by different SAMTools versions (0.1.18 and older ones) and also offers flexibility in dealing with vcf input files generated using SAMTools with two or three samples * The spreadsheet result file contains full protein sequences for both ref and alt alleles, which makes it easier for downstream protein structure/function analysis tools to take
Abbreviations: SNPAAMapper
Synonyms: SNPAAMapper - A SNP Amino Acid Mapping tool
Resource Type: data processing software, software resource, software application
Defining Citation: PMID:24250114
Keywords: single nucleotide polymorphism, amino acid, variant, annotation, exon, intron, mutation, next-generation sequencing, perl, downstream analysis, bio.tools
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