Closed DarioS closed 4 years ago
A DNP, such as CC > TT, is considered to be an indel:
is.indel <- ref_len > 1L | alt_len > 1L
It appears that the software considers anything that is not a SNP to be an indel. But DNP or TNP are not indels and I was confused at first to see:
ref.len <- nchar(fsnplist.indel[nchar(fsnplist.indel$REF) == nchar(fsnplist.indel$ALT)]$REF) # Indel variants same length as reference.
Could a better categorisation of variants be used, such as Simple Nucleotide Variants (SNV) and indels? Typically, the genomics abbreviations are:
SNP, single-nucleotide polymorphism; SNV, simple nucleotide variant
Hi, computationally we treat indels and serial substitutions (or however you want to label them) the same for purposes of calculation.
A DNP, such as CC > TT, is considered to be an indel:
It appears that the software considers anything that is not a SNP to be an indel. But DNP or TNP are not indels and I was confused at first to see:
Could a better categorisation of variants be used, such as Simple Nucleotide Variants (SNV) and indels? Typically, the genomics abbreviations are: