wget ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/phastConsElements46way.txt.gz
gunzip phastConsElements46way.txt.gz
mv phastConsElements46way.txt hg19_phastConsElements46way.txt
mv hg19_phastConsElements46way.txt /tomato/data
/tomato/app/annovar/convert2annovar.pl x1.pass.vcf -format vcf4 > x1.annovar
/tomato/app/annovar/annotate_variation.pl -regionanno --buildver hg19 -dbtype mce46way x1.annovar /tomato/data/
/tomato/app/annovar/annotate_variation.pl -downdb -buildver hg19 avsift .
mv hg19_avsift.txt* /tomato/data
/tomato/app/annovar/convert2annovar.pl x1.pass.vcf -format vcf4 > x1.annovar
/tomato/app/annovar/annotate_variation.pl -filter -buildver hg19 -dbtype avsift x1.annovar /tomato/data/
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