Question: Vcftools,Vcf-Merge Error
gravatar for Joanne Lim
7.3 years ago by
Joanne Lim0
Joanne Lim0 wrote:

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/ 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/ 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/ 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.


vcf vcftools • 5.8k views
ADD COMMENTlink modified 7.3 years ago by pd3340 • written 7.3 years ago by Joanne Lim0
gravatar for Maxime Lamontagne
7.3 years ago by
Maxime Lamontagne2.1k wrote: is a file present in vcftools_0.1.4a/lib.

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

I think this should solve your error.

ADD COMMENTlink written 7.3 years ago by Maxime Lamontagne2.1k
gravatar for Rlong
7.3 years ago by
Rlong340 wrote:

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]

ADD COMMENTlink modified 7.3 years ago • written 7.3 years ago by Rlong340

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!

ADD REPLYlink written 7.2 years ago by Joanne Lim20
gravatar for Joanne Lim
7.3 years ago by
Joanne Lim20
United Kingdom
Joanne Lim20 wrote:


My file is already in the path mentioned though.

ADD COMMENTlink written 7.3 years ago by Joanne Lim20

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..

ADD REPLYlink written 7.3 years ago by Rlong340
gravatar for pd3
7.2 years ago by
pd3340 wrote:

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

ADD COMMENTlink written 7.2 years ago by pd3340
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