Merge individual vcf files

[francy]

Dear SEQanswers,

I cannot get the Perl scripts in VCFtools called "vcf-merge" to work and would like to ask for your help.

This is my problem:
I have 5 VCF files I would like to merge, and I have converted each one to VCFv4.0 using the perl script in VCFtools/perl called "vcf-convert".
Then I used bgzip and tabix -p vcf as it is explained in the website.
I also changed the PATH to where the perl scripts are, like this:
"export PERL5LIB='/ugi/home/claudiagiambartolomei/shared/vcftools_0.1.5"

Finally, when I type "perl vcf-merge file1.vcf.gz.tbi file2.vcf.gz.tbi file3.vcf.gz.tbi file4.vcf.gz.tbi file5.vcf.gz.tbi | gzip -c > out_merged.vcf.gz "

First a lot of odd-looking signs and question marks come up, and then an error comes up which says:

], assuming VCFv4.0
Broken VCF header, no column names?
at /vcftools_0.1.5/perl//Vcf.pm line 169
Vcf::throw('Vcf4_0=HASH(0x25672d8)', 'Broken VCF header, no column names?') called at /vcftools_0.1.5/perl//Vcf.pm line 808
VcfReader::_read_column_names('Vcf4_0=HASH(0x25672d8)') called at /vcftools_0.1.5/perl//Vcf.pm line 583
VcfReader:arse_header('Vcf4_0=HASH(0x25672d8)') called at /vcftools_0.1.5/perl/vcf-merge line 128
main::init_cols('HASH(0x28a5b20)', 'Vcf4_0=HASH(0x2566b40)') called at /vcftools_0.1.5/perl/vcf-merge line 221
main::merge_vcf_files('HASH(0x28a5b20)') called at /vcftools_0.1.5/perl/vcf-merge line 12

Can you please help me figure out what I am doing wrong?

Thank you very much for any advice you could give me,
-f

[iansealy]

It looks like you're trying to merge the tabix index files rather than the VCF files. Try something like:

perl vcf-merge file1.vcf.gz file2.vcf.gz file3.vcf.gz file4.vcf.gz file5.vcf.gz > out_merged.vcf

Cheers,
Ian

[pbluescript]

I can't help with vcftools, but bedtools supports vcf files if you want to give that a shot.

[francy]

Thank you very much to both for your replies!
iansealy, it worked: I just needed to do run the command using the files not indexed using tabix! Although I am not sure why since it states clearly in the perl script "Merge the bgzipped and tabix indexed VCF files. (E.g. bgzip file.vcf; tabix -p vcf file.vcf.gz)\n"
...Anyway using only the .gz works!!

pbluescript, I didn't know about bedtools and since I'll do much of this in the future I am sure I'll need that too so thanks for mentioning it.

Cheers,
-f

[ulz_peter]

When you index a file using tabix (or what ever tool) it creates an index which is used together withthe file itself. The .tbi files are not the indexed vcf file but extra index files (every .vcf file needs an additional .vcf.tbi file). You need to create the indexes but you need to specify the vcf (in this case gzipped vcf.gz) files. The program recognises the index files by just adding the .tbi to the file name you specified.
That's like a general rule for the tools which need indexed files. You create the index file but you specify the normal file and the program searches for the index files itself...

I hope this clarifies it.

[francy]

Dear ulz peter,

Thank you for explaining this, it finally makes sense now!

cheers,
-f