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

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?

vcf vcftools

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updated 5.8 years ago by Biostar

• written 13.2 years ago by Sheila

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

• 0 views • link

written 13.2 years ago by Giovanni M Dall'Olio

I'm installing on a linux environment. I downloaded the tarball from the vcftools website (version 0.1.10), unpacked it, cd'd into the vcftools directory, and typed "make". What am I missing? Thanks. http://vcftools.sourceforge.net/docs.html#install

• 0 views • link

written 13.2 years ago by Sheila

2 answers

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/

• 0 views • link

updated 6.6 years ago by Ram

• written 13.2 years ago by Giovanni M Dall'Olio

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.

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updated 6.6 years ago by Ram

• written 13.2 years ago by Sheila

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.

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written 13.2 years ago by Giovanni M Dall'Olio

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

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written 13.2 years ago by Sheila

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.

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written 13.2 years ago by Giovanni M Dall'Olio

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

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written 13.1 years ago by Sheila

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?

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updated 6.6 years ago by Ram

• written 13.2 years ago by Robert Sicko