VcfCodingSnps
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vcfCodingSnps is a variant annotation tool (still unpublished as of july 2013) that annotates genetic variants such as single nucleotide polymorphisms (SNPs) and short insersion and deletions (INDELs) in a VCF format input file. It takes a VCF as an input and generates an annotated VCF file as an output [1].
Definition used in vcfCoding Snps
- stop gained: a SNP in coding sequence and introducing a TAG, TAA, or TGA stop codon
- stop lost: a SNP in coding sequence and causing a loss of a TAG, TAA, or TGA stop codon
- non-synonymous coding: a SNP in coding sequence, located in a codon resulting in a change of amino acid, excluding SNPs that can be defined as either stop gained or stop lost
- synonymous coding: a SNP in coding sequence, located in a codon that not resulting in a change of amino acid
- essential splice site: a SNP changing the highly conserved GU in the first two basepairs of the intron or (AG) in the last two basepair of the intron
- splice site: a SNP occurring in 3 - N1 basepairs into the intron, or N2 basepairs into the exon . N1 by default is 8, N2 by default is 3. N1 and N2 can be defined by user through option --n1 --n2.
- 5' UTR: a SNP located within the 5' UTR of a transcript
- 3' UTR: a SNP located within the 3' UTR of a transcript
- intronic: a SNP in the intron of a known gene, and cannot be defined as essential splice site or splice site
- upstram: a SNP located within N kb from the transcript start site (5'-end) of a known gene, N by default is 5 and can be defined by user through option --ns
- downstream: a SNP located within N kb from the transcript end site (3'-end) of a known gene, N by default is 5 and can be defined by user through option --ns
- introgenic: a SNP not located within a known gene and also not identified as upstream or downstream of a knowngene
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