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ExmRes.1.ANNOVAR_download_databases.sh
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#!/bin/bash
dbToDownload=$1
AnnovarDirectory=/ifs/scratch/c2b2/af_lab/ads2202/bin/annovar
latest1KG=1000g2014oct
latestdbSNP=snp138
latestLJB=ljb26_all
latestESPall=esp6500siv2_all
latestESPaa=esp6500siv2_aa
latestESPea=esp6500siv2_ea
latestCOMIC=cosmic70
cd $AnnovarDirectory
case $dbToDownload in
1)
nam="Download: refseq hg19 gene reference"
cmd="perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar refGene humandb/"
;;
2)
nam="Download: 1000 genomes reference"
cmd="perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar $latest1KG humandb/"
;;
3)
nam="Download: dbSNP reference"
cmd="perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar $latestdbSNP humandb/"
;;
4)
nam="Download: LJB"
cmd="perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar $latestLJB humandb/"
;;
5)
nam="Download: ESP alternative allele frequency - all"
cmd="perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar $latestESPall humandb/"
;;
6)
nam="Download: ESP alternative allele frequency - African Americans"
cmd="perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar $latestESPaa humandb/"
;;
7)
nam="Download: SP alternative allele frequency - European Americans"
cmd="perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar $latestESPea humandb/"
;;
8)
nam="Download: superdups "
cmd="perl annotate_variation.pl -downdb -buildver hg19 genomicSuperDups humandb/"
;;
9)
nam="Download: Cadd top 10% "
cmd="perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar caddgt10 humandb/"
;;
10)
nam="Download: Cadd indel "
cmd="perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar caddindel humandb/"
;;
11)
nam="Download: exac03"
cmd="perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar exac03 humandb/"
;;
12)
nam="Download: Cadd full "
cmd="perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar cadd humandb/"
;;
13)
nam="Download: Cadd full "
cmd="perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar clinvar_20150330 humandb/"
;;
14)
nam="Download: COSMIC "
cmd="perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar $latestCOMIC humandb/"
;;
esac
echo "Start $nam - `date`"
echo $cmd
eval $cmd
if [[ $? == 0 ]]; then
echo "Finish $nam - `date`"
else
echo "Error during "${nam/load:/loading}
fi