annovar.pl

#!/usr/bin/perl
### Annovar ###
use Getopt::Std;

sub Usage{
    print STDERR <<EOF;
    Usage: annovar.pl -t <number of threads> -i <sample name>  -r <reference version> -o <annotation output>

    Command:
             -i	 sample file convert to annovar format (Example: *.avinput)
             -t  number of threads
             -r  reference version (hg19 / hg38)
             -o	 sample file annotation output

EOF
    exit;
}
my %opt;
getopt("i:t:r:o:", \%opt);
my $input = $opt{i} or &Usage();
my $num_threads = $opt{t} or &Usage();
my $rf = $opt{r} or &Usage();
my $output = $opt{o} or &Usage();
my $PATH = '$HOME/2019GenomicsEpidemiologyWorkshop/annovar/';
my $DB_PATH = '$HOME/humandb/';


`$PATH/table_annovar.pl --thread $num_threads $input $DB_PATH -buildver $rf -out $output -remove -protocol refGene,ensGene,cytoBand,genomicSuperDups,gwasCatalog,avsnp150,esp6500siv2_all,1000g2015aug_all,1000g2015aug_afr,1000g2015aug_amr,1000g2015aug_eur,1000g2015aug_eas,1000g2015aug_sas,nci60,cosmic89_coding,cosmic89_noncoding,clinvar_20190305,gnomad211_genome,gnomad211_exome,exac03,intervar_20180118,dbnsfp31a_interpro -operation g,g,r,r,r,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f,f -otherinfo -nastring NA`;

print STDERR "Finished\n";