What is SNP and indel?
What is SNP and indel?
By definition, an SNP changes a single nucleotide in the DNA sequence, whereas an indel incorporates or removes one or more nucleotides (Loewe, 2008). SNPs in coding and noncoding regions have been implicated in both Mendelian and complex disease, and the same is true for indels.
What is Minimap2?
Minimap2 is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database.
What is meant by low complexity region of a sequence?
Low-complexity regions (LCRs) are amino acid sequences that contain repeats of single amino acids or short amino acid motifs. They are extremely abundant in eukaryotic proteins (Green and Wang 1994; Golding 1999; Marcotte et al. 1999).
What are low complexity regions genome?
Low-complexity regions are often defined as regions of biased composition containing simple sequence repeats (1). A sequence enriched with imperfect direct and inverted repeats may also be considered as a sequence with low complexity (5).
What does indel stand for?
“Indel” is a general term that may refer to insertion, deletion, or insertion and deletion of nucleotides in genomic DNA.
What is indel calling?
Calling indel from the mpileup file: Pindel [32] (version 0.2.4) is a pattern growth approach-based tool that detects breakpoints of large deletions, medium-sized insertions, and other structural variants from NGS data at single-based resolution. In Pindel, all reads are initially mapped to the reference genome.
What is the output of Minimap2?
Input/output options
| -a | Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF by default. |
|---|---|
| Output the cs tag. STR can be either short or long. If no STR is given, short is assumed. [none] | |
| –MD | Output the MD tag (see the SAM spec). |
| –eqx | Output =/X CIGAR operators for sequence match/mismatch. |
What does low complex mean?
adjective Referring to a region of protein sequence enriched with a single amino acid.
What is a low complexity protein domain?
Low-complexity domains (LCDs) in protein sequences are unusual regions made up of only a few different types of amino acids. Although this is the key feature that classifies sequences as LCDs, the physical properties of LCDs will differ based on the types of amino acids that are found in each domain.
What is indel formation?
An indel inserts or deletes nucleotides from a sequence, while a point mutation is a form of substitution that replaces one of the nucleotides without changing the overall number in the DNA. Indels can also be contrasted with Tandem Base Mutations (TBM), which may result from fundamentally different mechanisms.
https://www.youtube.com/watch?v=ro8qtZRf-K4
