vcftools perl script

[weiyulin]

I managed to compare the vcf files between two samples using vcftools perl script. However, I got the error messages in the following. It seems to do with the index file. What does it mean? Does this mean the index file is not in the correct format or anything I did it in a wrong way?
Your help is greatly appreciated

compare-vcf 441_M1_1x_SNP.vcf 441_2x_SNP.vcf
[main] fail to load the index file.
The command "tabix -l 441_M1_1x_SNP.vcf" exited with an error. Is the file tabix indexed?
at /home/weiyu/Downloads/VCFtools/lib/Vcf.pm line 422
Vcf::throw('Vcf4_0=HASH(0x9764fc8)', 'The command "tabix -l 441_M1_1x_SNP.vcf" exited with an error...') called at /home/weiyu/Downloads/VCFtools/lib/Vcf.pm line 1547
Vcf::get_chromosomes('Vcf4_0=HASH(0x9764fc8)') called at /home/weiyu/Downloads/VCFtools/bin/compare-vcf line 100
main::compare_vcfs('HASH(0x961c818)') called at /home/weiyu/Downloads/VCFtools/bin/compare-vcf line 12
weiyu@weiyu-VIG555M:~/test_for_vcf_snp$ tabix -l 441_M1_1x_SNP.vcf
[main] fail to load the index file.

[ashokrags]

make sure tabix is in your bin

[ashokrags]

and also you need to index the files with tabix and then copy the .tbi and .idx files to the directory

[weiyulin]

Thanks a lot!

It's working well now

[johnadam33]

Hi Weiyulin and Ashok,
I am very new to this VCF files and perl. I am also trying to do the same thing, compare the variants with my own data. how can I proceed or for someone who has no idea what pearl is, is there are place where u can find help with this data?
Thanks,
John.

[ashokrags]

Hi John,
I think that you need to do some research and familirize yourself with the research tools out there. There are many tools and i think it depends on your question and the platform you are using e.g. SOLID or illumina. Perl by itself may not be necessary to learn until you start doing data processing operations and then there are a host of scripting languages out there Perl, Python, R, Ruby, etc etc and your choice is a matter of preference. I wish I could be of more help, but this is really a vast topic and depending on the level of your knowledge the answers are going to vary.
good luck

[johnadam33]

Hi Ashok. Thanks for the reply. I have no background in perl or any other ones. I am trying to access the VCF files from 1000 genomes. I am assuming that's what u are talking about when u said comparing two vcf files. So in order for the vcf tools to work, I should extract them to the folder that has the perl program? Also the same with tabix? What is indexing and also how do u set that in linux?