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  • Creating index for Annovar database file

    Hi,

    Anybody has idea how to create index file for the Annovar annotation database files.

    I am running Annovar with snp135_NonFlagged annotation file and it is taking a lot of time compared to snp135 which has .idx file.

    Thanks

  • #2
    Creating Annovar Index

    The Annovar idx format is as follows:

    1. File is tab separated.

    2. First Line: #BIN <BiN SIZE> <File Size>

    3. Remaining lines:
    <Chromosome> <BIN Starting Position> <Starting position in File> <Ending position in File>

    In Perl, the following routine would create the index of the file in a hash (dictionary/map), then you'd just need to print it out:

    Code:
    #!/usr/bin perl;
    use warnings;
    use strict;
    
    die "$0 <Annovar Database File> <BIN Size>" unless @ARGV == 2;
    my $input_file = $ARGV[0];
    my $bin_size = $ARGV[1];
     
    if (!-e $input_file) {
    	die "$input_file not found\n";
    }
    
    my $file_size = -s $input_file;
    
    my %index;
    open(my $in, "<", $input_file) or die "Couldn't open $input_file for indexing\n";
    
    my $previous_file_position = tell $in;
    
    while (my $ln = <$in>) {
    	
    	#Check input file. Some are (chr,start,stop) and others are (id,chr,start,stop).
    	#If you have the latter you'll need to change the next line to account for the id column   
    	my ($chr,$start,$stop) = split "\t", $ln;
    	my $bin_start = int($start/$bin_size) * $bin_size;
    	my $current_file_position = tell $in;
    
    	if (!exists $index{$chr}->{$bin_start}) {
    		$index{$chr}->{$bin_start} = [$previous_file_position, $current_file_position];
    	}
    	else{
    		$index{$chr}->{$bin_start}->[1] = $current_file_position;
    	}
    	
    	$previous_file_position = $current_file_position;
    }
    
    close $in;
    
    print "#BIN\t$bin_size\t$file_size\n";
    foreach my $chr ((1,10..19,2,20,21,22,3..9,"MT","X","Y")){ #Ordered array to match other Annovar idx files
    	foreach my $index_region (sort keys %{$index{$chr}}){
    		my $start	= $index{$chr}->{$index_region}->[0];
    		my $stop	= $index{$chr}->{$index_region}->[1];
    		print "$chr\t$index_region\t$start\t$stop\n";
    	}
    }
    I've checked the output against a couple idx files (clinvar20140702, AFR.sites.2012) provided by Annovar and get perfect agreement.
    Last edited by lottpaul; 05-29-2015, 07:42 AM. Reason: Complete Code

    Comment


    • #3
      The script is not working for me. I get an error message ("$current_position" requires explicit package name). After changing $current_position to $current_file_position in line 27, I get error messages 'Argument "chr4" isn't numeric in division (/) at ./makeannovarindex.pl line 23, <$in> line 20493.'

      then I change line 22 from
      my ($chr,$start,$stop) = split "\t", $ln;
      to
      my ($junk,$chr,$start,$stop) = split "\t", $ln;

      the errors stop, but get no output (except for line 1: "#BIN 1000 24679810")

      Does anybody experience the same issues? Could anyone get this script working?

      Comment


      • #4
        Hi,

        First of, thanks to lottpaul for providing the solutions.

        I have modified a line or two, I suppose. So I am attaching the script that I used finally.

        Following is the command, I used to run the script.

        Code:
        perl compileAnnnovarIndex.pl hg19_snp138NonFlagged.txt 1000 > hg19_snp138NonFlagged.txt.idx
        I hope it works for you too.
        Attached Files

        Comment

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