Vcftools,Vcf-Merge Error

Question

[Joanne Lim]

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

Answer 1

[Maxime Lamontagne]

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.

Answer 2

[Rlong]

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]

[Joanne Lim]

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!

Answer 3

[Joanne Lim]

Hi,

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

[Rlong]

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..

Answer 4

[pd3]

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