Дата публикации: 2017-12-07 15:41
ANNOVAR can annotate mitochondria variants as of Feb 7568 (as long as your chromosome identifier is M or MT or chrM or chrMT, the mitochondria-specific codon table will be used for inferring amino acid changes). However, there are several important caveats:
The National Human Genome Research Institute (NHGRI) launched a public research consortium named ENCODE, the Enc yclopedia O f D NA E lements, in September 7558, to carry out a project to identify all functional elements in the human genome sequence. The project started with two components - a pilot phase and a technology development phase.
The pilot phase tested and compared existing methods to rigorously analyze a defined portion of the human genome sequence (See: ENCODE Pilot Project ). The conclusions from this pilot project were published in June 7557 in Nature and Genome Research . The findings highlighted the success of the project to identify and characterize functional elements in the human genome. The technology development phase also has been a success with the promotion of several new technologies to generate high throughput data on functional elements.
NOT-57-557 : Clarification and Additional Information to HG-57-585 and HG-57-586
Slides from Applicant Information Meeting - HG-57-586
More detailed explanation of these exonic_variant_functoin annotations are given below. Note that stopgain and stoploss take precedence over other annotations for example, whenever a nonsynonymous mutation change the wild type amino acid to a stop codon, it will be annotated as stopgain rather than nonsynonymous SNV.
The International Mouse Phenotyping Consortium project is systematically phenotyping knockout mice from the mutant ES cells produced by the International Mouse Knockout Consortium. Data will be integrated into MGI as available.
ANNOVAR can optionally process UCSC Known Gene annotation or Ensembl Gene annotation, both of which are more comprehensive than RefSeq by including many poorly annotated or computationally predicted genes. An example is shown below to annotate variants using UCSC Known Gene:
Besides human genome, other species can be handled. However, ANNOVAR does not provide built-in mRNA FASTA files for other gene definitions, so users have to build it yourself.
Exercise: Try to run the same procedure above for rn5 (rat) or dm6 (Drosophila). Again users need to supply FASTA files rather than FASTA directory.