Error When Merging Vcfs With Vcftools'S Vcf-Merge Function

Question

[Sheila]

I'm getting an error when i attempt to merge 3 vcfs with VCFtools' vcf-merge function. See below:

COMMAND:

 /ifshome/vcftools_0.1.10/bin/vcf-merge *.vcf > combinedVCF.vcf

OUTPUT:

Can't locate Vcf.pm in @INC (@INC contains: /usr/local/mni/lib /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /ifshome/vcftools_0.1.10/bin/vcf-merge line 9.
BEGIN failed--compilation aborted at /ifshome/pbhatt/vcftools_0.1.10/bin/vcf-merge line 9.

What is the problem here?

Answer 1

[Giovanni M Dall'Olio]

the error message is telling you that vcftools is not installed properly. How did you install it? In which system you are working?

If you want a quick and dirty fix, locate the folder lib/perl5/site_perl in which you have downloaded vcftools, write down the full path to it, and then add the following line to your ~/.bashrc file:

export PERL5LIB=$PERL5LIB:/path/to/vcftools/lib/perl5/site_perl/

[Sheila]

Thanks! I'm getting a different error now:

/ifshome/pbhatt/vcftools_0.1.10/bin/vcf-merge *.vcf > combinedVCF.vcf.gz
Broken VCF header, no column names?
 at /ifshome/pbhatt/vcftools_0.1.10/lib/perl5/site_perl//Vcf.pm line 177
    Vcf::throw('Vcf4_1=HASH(0xbb1f280)', 'Broken VCF header, no column names?') called at /ifshome/pbhatt/vcftools_0.1.10/lib/perl5/site_perl//Vcf.pm line 869
    VcfReader::_read_column_names('Vcf4_1=HASH(0xbb1f280)') called at /ifshome/pbhatt/vcftools_0.1.10/lib/perl5/site_perl//Vcf.pm line 604
    VcfReader::parse_header('Vcf4_1=HASH(0xbb1f280)') called at /ifshome/pbhatt/vcftools_0.1.10/bin/vcf-merge line 181
    main::init_cols('HASH(0xbb18a10)', 'Vcf4_1=HASH(0xbb19380)') called at /ifshome/pbhatt/vcftools_0.1.10/bin/vcf-merge line 277
    main::merge_vcf_files('HASH(0xbb18a10)') called at /ifshome/pbhatt/vcftools_0.1.10/bin/vcf-merge line 12

Not sure what this is either... sorry I'm very new to this.

[Giovanni M Dall'Olio]

Your vcf file doesn't contain headers. How did you get it? If you downloaded it using tabix, remember to add the -h option, to include the headers as well.

[Sheila]

I received these VCFs straight from Illumina and when I open the file itself in my favorite text editor I see the headers.

[Giovanni M Dall'Olio]

Check the files again. At least one file in your folder is missing the column headers. The last line before the data must begin with #CHROM, followed by 9 columns, and then one column per individual.

[Sheila]

I've looked and both have the header column. Could it be a size issue? My VCF files are very large.

Answer 2

[Robert Sicko]

vcftools,vcf-merge error

similar error in the above post mentions possible solutions.

I have not used vcftools, but I did want to mention I've used Pierre's scanvcf to merge a bunch of VCF's from different subjects: A: How can I merge a large amount of VCF files?