Annovar

Annovar Annotation
 * 1000 Genomes Project Phase I (release v3 - 2012/04/30) annotation for Annovar
 * 1000genomes_to_Annovar (How-To)
 * Annovar update

- simple annotation - 

perl annotate_variation.pl --downdb --buildver hg19 refGene humandb perl annotate_variation.pl --downdb --buildver hg19 knownGene humandb perl annotate_variation.pl --downdb --buildver hg19 ensGene humandb perl annotate_variation.pl --downdb --buildver hg19 1000g humandb/ perl annotate_variation.pl --downdb --buildver hg19 snp132 humandb/ perl annotate_variation.pl --downdb --buildver hg19 avsift humandb/ perl annotate_variation.pl --downdb --buildver hg19 1000g2012feb humandb/ perl annotate_variation.pl --downdb --buildver hg19 ljb_all --webfrom annovar  humandb/ annotate_variation.pl --downdb --buildver hg19 esp5400_ea -webfrom annovar humandb/ annotate_variation.pl --downdb --buildver hg19 esp5400_all -webfrom annovar humandb/ annotate_variation.pl --downdb --buildver hg19 genomicSuperDups humandb/ annotate_variation.pl --downdb --buildver hg19 phastConsElements46way humandb/

perl  /path/to/annovar/summarize_annovar.pl   --verdbsnp 135    --buildver hg19     \ /path/to/humandb  input.bed   --outfile   output_sum

10	100013368	100013368	G	A 10	100013438	100013438	C	T 10	100016575	100016575	G	A 10	100016700	100016700	C	T 10	100017453	100017453	T	G
 * 1) input bed file #########

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