This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Vcftools,Vcf-Merge Error

I had run vcftools to merge some vcf files with no success. As mentioned, the *.vcf files was pre-processed with bgzip and tabix.

Here are my commands for (bgzip,tabix and vcftools)

./bgzip fileA.vcf

./bgzip fileB.vcf

./bgzip fileC.vcf

./tabix -p vcf fileA.vcf.gz

./tabix -p vcf fileB.vcf.gz

./tabix -p vcf fileC.vcf.gz

vcf-merge fileA.vcf.gz fileB.vcf.gz fileC.vcf.gz >out.vcf.gz

Here's the error after I run the vcf-merge command :-

The use of -1 for unknown number of values is deprecated, please use '.' instead. FORMAT=<ID=PL,Number=-1,Type=Integer,Description="List of="" Phred-scaled="" genotype="" likelihoods,="" number="" of="" values="" is="" (#ALT+1)*(#ALT+2)="" 2"=""> Can't exec "tabix": No such file or directory at /usr/lib64/perl5/5.8.8/x8664-linux-thread-multi/Vcf.pm line 2155. The command "tabix -l raws51sequenceBWT.vcf.gz" exited with an error. Is the file tabix indexed?

at /usr/lib64/perl5/5.8.8/x8664-linux-thread-multi/Vcf.pm line 171 Vcf::throw('Vcf41=HASH(0xb762650)', 'The command "tabix -l raws51sequenceBWT.vcf.gz" exited w...') called at /usr/lib64/perl5/5.8.8/x8664-linux-thread-multi/Vcf.pm line 2156 VcfReader::getchromosomes('Vcf41=HASH(0xb762650)') called at /illumina/MiniProject/tools/vcftools0.1.7/perl/vcf-merge line 165 main::initcols('HASH(0xb760710)', 'Vcf41=HASH(0xb761ff0)') called at /illumina/MiniProject/tools/vcftools0.1.7/perl/vcf-merge line 245 main::mergevcffiles('HASH(0xb760710)') called at /illumina/MiniProject/tools/vcftools_0.1.7/perl/vcf-merge line 12

I am currently using linux, with tabix-0.2.5 and vcftools_0.1.7 (if this helps)

Thanks in advance.

Joanne

vcftools vcf vcf
• 9,901 views • link
updated by pd3 pd3 • written by Joanne Lim • Joanne Lim

4 answers

Vcf.pm is a file present in vcftools_0.1.4a/lib.

You need to copy Vcf.pm in /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/.

I think this should solve your error.

• 2 views • link
written by Maxime Lamontagne Maxime Lamontagne

I've never had much luck with vcf-tools. You may have better luck with joinx. Once you have it installed, you should be able to use this command:

joinx vcf-merge fileA.vcf fileB.vcf fileC.vcf -o mergedFile.vcf

Or, if you have them bgzipped already:

joinx vcf-merge <(zcat fileA.vcf.gz) <(zcat fileB.vcf.gz) <(zcat fileC.vcf.gz) | bgzip -c > output file

I realize "use a different program" might not be the answer you're looking for, but vcf-tools doesn't seem to handle the full range of allowable formatting in vcf. [edited]

• 2 views • link
written by Rlong • Rlong

I've checked that it is a vcf file. I'll try joinx, but it seems like its more for ubuntu? I am actually using Fedora and is currently facing this issue with this error,"E: Couldn't Find Package Libboost-all-dev" during the installation,which was after I've build the Boost library. Any idea if Joinx works on Fedora? Many thanks!

• 0 views • link
written by Joanne Lim • Joanne Lim

Hi,

My Vcf.pm file is already in the path mentioned though.

• 0 views • link
written by Joanne Lim • Joanne Lim

Are you sure that "raw_s_5_1_sequence_BWT.vcf.gz" is a proper vcf and not a BAM or something else? It looks like the forward reads from lane 5 off of a flow cell..

• 0 views • link
written by Rlong • Rlong

Did you try to run vcf-validator to check that the your files are valid?

• 0 views • link
written by pd3 pd3

Log in to answer this question.

More posts like this
  • VCF-merge fails due to tabix not producing .tbi files
    written by brallen • brallen
    I'm trying to use vcf-merge to combine 2 exome capture vcf files (~250K and ~330K in size) before trying it on all 96 samples. I'd …
  • Problem with vcf-merge
    written by vncnt.anna • vncnt.anna
    Hi I am trying to merge two VCFs which I got from using platypus joint variant calling on bam files which I had to split …
  • Broken vcf header, no column name?
    written by samuel.lipworth • samuel.lipworth
    Hi, Trying to use VCF tool's vcf-compare function. I have bgzipped and tabixed indexed my files bgzip -c file.vcf > file.vcf.gz tabix -p vcf file.vcf.gz …
  • Problems with vcf-merge
    written by devenvyas devenvyas
    I have a list of SNPs from an old Illumina array. I've concatenated and filtered two sets of VCF files (http://cdna.eva.mpg.de/neandertal/altai/AltaiNeandertal/VCF/, http://cdna.eva.mpg.de/denisova/VCF/hg19_1000g/) from two diploid …
  • Vcf Tools Error
    written by tpeters1213 • tpeters1213
    <p>I'm working on a project that involves merging four VCF files. The first three datasets ran smoothly through vcftools' vcf-merge, but merging the final dataset …
  • Error When Merging Vcfs With Vcftools'S Vcf-Merge Function
    written by Sheila Sheila
    <p>I'm getting an error when i attempt to merge 3 vcfs with VCFtools' vcf-merge function. See below:</p> <p>COMMAND:</p> <pre><code> /ifshome/vcftools_0.1.10/bin/vcf-merge *.vcf &gt; combinedVCF.vcf </code></pre> <p>OUTPUT: …
  • Vcf-Tools : Error "Broken Vcf Header, No Column Names?'"
    written by Pierre Lindenbaum Pierre Lindenbaum
    <p>I've indexed a set of vcf with tabix.</p> <pre><code>$ gunzip -c A.vcf.bgz ##fileformat=VCFv4.1 (...) #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A chr1 …
  • Vcf-Compare Vcftools Error
    written by Leandro Batista • Leandro Batista
    <p>Hello,</p> <p>I'm using VCFtools to compare 2 different vcf files. When I run vcf-compare with the following command:</p> <p><em>vcf-compare Software/snpEff/chr11snps.vcf.gz Software/snpEff/chr11snps_output.vcf.gz</em></p> <p>I get the following …
  • Vcftools: Vcf-Merge How To Run ?
    written by Deniz • Deniz
    <p>[perl]$ ./vcf-merge 1.flt.vcf.gz 2.flt.vcf.gz 3.flt.vcf.gz 4.flt.vcf.gz 5.flt.vcf.gz 6.flt.vcf.gz 7.flt.vcf.gz 8.flt.vcf.gz 9.flt.vcf.gz 10.flt.vcf.gz 11.flt.vcf.gz | bgzip -c &gt; merged.vcf.gz </p> <p>-bash: bgzip: command not found The …
  • Help On Merging Vcf Files By Using Vcftools
    written by Jianfengmao • Jianfengmao
    <p>Dear BioStarers,</p> <p>I am learning VCFtools by executing VCFtools commands on VCF files in Examples folder of the VCFtools installation path. </p> <p>Please help me …