Nel Anno del Dragone è un gioco ideato da Stefan Feld e pubblicato da Alea. I giocatori assumono il ruolo di sovrani cinesi intorno all'anno 1000. Il gioco si svolge in dodici round, con ogni round che rappresenta un mese in un anno che sembra andare di male in peggio. Malattie, siccità e attacchi dei Mongoli possono costare vite, ma assicurati di avere abbastanza soldi per offrire un tributo all'Imperatore. Il gioco è più facile di quanto possa sembrare. Ogni giocatore ha un set di carte "persona". Ogni round, scegli un'azione (la maggior parte delle quali fa affidamento sulle capacità dei tuoi lavoratori) per aiutarti a prepararti per i mesi a venire. Quindi giochi una carta persona, reclutando quella persona e piazzandola in uno dei tuoi palazzi. Ogni persona porta abilità e abilità diverse per aiutarti a superare l'anno. (Gli agricoltori ti aiutano a guadagnare riso per sopravvivere a un mese di siccità, gli Esattori delle Tasse raccolgono fondi, ecc.) Alla fine di ogni round, viene attivato l'evento di quel mese, che potrebbe costarti alcuni dei tuoi lavoratori, dei soldi o darti punti. Un'attenta pianificazione è la chiave per sopravvivere "all'anno del dragone", ma la sopravvivenza da sola potrebbe non farti vincere la partita.
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ANNOVAR can identify the variant that are already reported in dbSNP and also identify the corresponding rs identifiers. To speed up dbSNP annotation, ANNOVAR provides pre-built indexed files in its database repository. Use -webfrom annovar in the command to download these files for use in annotation procedure. Only a few specific versions of dbSNP have been made available, so check download page for these specific versions. Finally, I wrote an article on dbSNP identifiers, and you are welcome to read and comment on it.
The keyword used for downloading these data include: ljb23_sift, ljb23_pp2hdiv, ljb23_pp2hvar, ljb23_lrt, ljb23_mt, ljb23_ma, ljb23_fathmm, ljb23_metasvm, ljb23_metalr, ljb23_gerp++, ljb23_phylop, ljb23_siphy, ljb23_all. The ljb23_all includes ALL scores, and it is very useful in table_annovar.pl.
The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a wide variety of large-scale sequencing projects. The allele frequency information for the ExAC can be downloaded using exac02, exac03 keywords in ANNOVAR. Currently supported population groups include ALL, AFR (African), AMR (Admixed American), EAS (East Asian), FIN (Finnish), NFE (Non-finnish European), OTH (other), SAS (South Asian)).
The commands above first download the "cg46" database to the humandb/ directory, then scan the ex1.avinput file against the database. Variants that are found in cg46, as well as their allele frequencies, are written to the *dropped file:
I compiled the database to be used by ANNOVAR. Note that the database name has a date (which is identical to Clinvar release date) as suffix, so make sure to check the download page to use the latest version.
CADD (Combined Annotation Dependent Depletion) is a score that is based on SVM on multiple other scores. One nice thing about it is that it assigns a score to each possible mutation in the human genome, therefore can evaluate non-coding variants as well as coding ones. The problem with this database is that the size is just too big (350GB in ANNOVAR format). However, several ANNOVAR users requested that I make it available through ANNOVAR, so that they can realistically use CADD in their exome sequencing studies. Therefore, I made the database available in Februray 2014 to ANNOVAR users. Download it by -downdb cadd -buildver hg19, but before you download/use it, make sure that you have the appropriate license to use it (contact the authors themselves to obtain the license). Unfortunately I do not have the resources to make hg18 scores available.
Note that the prepare_annovar_user.pl file can be downloaded from here. The final result file should contain coding mutations from COSMIC, as well as the number of occurrences in different tumor types (However, note that these include both targeted screen and genome screen. If you only want genome screen, you should use the CosmicGenomeScreensMutantExport.tsv.gz file instead).
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