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Old 09-21-2012, 05:23 AM   #1
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Question Creating index for Annovar database file


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.

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Old 11-20-2014, 09:56 AM   #2
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Default 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:

#!/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];
		$index{$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 at 08:42 AM. Reason: Complete Code
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Old 05-28-2015, 02:37 AM   #3
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The script is not working for me. I get an error message ("$current_position" requires explicit package name). After changing $current_position to $current_file_position in line 27, I get error messages 'Argument "chr4" isn't numeric in division (/) at ./ line 23, <$in> line 20493.'

then I change line 22 from
my ($chr,$start,$stop) = split "\t", $ln;
my ($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?
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Old 05-28-2015, 05:05 AM   #4
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Location: Italy

Join Date: Nov 2011
Posts: 5


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.

perl hg19_snp138NonFlagged.txt 1000 > hg19_snp138NonFlagged.txt.idx
I hope it works for you too.
Attached Files
File Type: pl (1.2 KB, 438 views)
canisirius is offline   Reply With Quote

annovar, indexing, snp

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