./annotate_variation.pl -downdb -buildver hg19 gene humandb
./annotate_variation.pl -downdb -buildver hg19 knownGene humandb
./annotate_variation.pl -downdb -buildver hg19 ensGene humandb

./annotate_variation.pl -downdb -buildver hg19 band humandb/
./annotate_variation.pl -downdb -buildver hg19 tfbs humandb/
./annotate_variation.pl -downdb -buildver hg19 mce28way humandb/
./annotate_variation.pl -downdb -buildver hg19 segdup humandb/
./annotate_variation.pl -downdb -buildver hg19 mirna humandb/
./annotate_variation.pl -downdb -buildver hg19 mirnatarget humandb/
./annotate_variation.pl -downdb -buildver hg19 evofold humandb/
./annotate_variation.pl -downdb -buildver hg19 dgv humandb/
./annotate_variation.pl -downdb -buildver hg19 omimgene humandb/
./annotate_variation.pl -downdb -buildver hg19 gwascatalog humandb/
./annotate_variation.pl -downdb -buildver hg19 phastConsElements28wayPlacMammal humandb/

./annotate_variation.pl -downdb -buildver hg18 1000g humandb/
./annotate_variation.pl -downdb -buildver hg18 snp130 humandb/
./annotate_variation.pl -downdb -buildver hg18 avsift humandb/
./annotate_variation.pl -downdb 1000g2010 humandb/
./annotate_variation.pl -downdb 1000g2010jul humandb/
./annotate_variation.pl -downdb -buildver hg19 1000g2010nov humandb/

./annotate_variation.pl -downdb -buildver hg19 1000g2011may humandb/


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./convert2annovar.pl /seppdata/sepp/linkage/release/ALL.wgs.merged_beagle_mach.20101123.snps_indels_svs.sites.vcf -format vcf4 > 1000g20101123.txt


NOTICE: for SNPs, column 6 and beyond MAY BE heterozygosity status, quality score, read depth, RMS mapping quality, quality by depth, if these information can be recognized automatically
NOTICE: for indels, column 6 and beyond MAY BE heterozygosity status, quality score, read depth, read count supporting indel call, RMS mapping quality, if these information can be recognized automatically
NOTICE: Read 40664060 lines and wrote 0 different variants at 40664032 genomic positions (36820992 SNPs and 3843040 indels)
NOTICE: Among 40664032 different variants at 40664032 positions, 0 are heterozygotes, 0 are homozygotes
NOTICE: Among 36820992 SNPs, 25170172 are transitions, 11650820 are transversions

./annotate_variation.pl 1000g20101123.txt -buildver hg19 humandb/



./annotate_variation.pl -dbtype tfbs -regionanno 1000g20101123.txt -buildver hg19  humandb/





./annotate_variation.pl -dbtype bed -bedfile hg19_neanderthalSNPs_chr1.txt -regionanno 1000g20101123.txt -buildver hg19  humandb/




./annotate_variation.pl -dbtype bed -bedfile hg19_neanderthalSNPs.txt -regionanno 1000g20101123.txt -buildver hg19  humandb/

mv 1000g20101123.txt.hg19_bed neanderthalSNPs.txt