The bcftools/htslib VCF commands - Download and installation

Question

[chengyi31000]

I have much VCF files of sequencing data. (one sample one VCF) And I want to merge it together.I find that vcftools can do this,

perl vcf-merge /home/chung/seqdataQC/NGS2015011B_S1.genome.vcf.gz \
    /home/chung/seqdataQC/NGS2015011D_S1.genome.vcf.gz \
    /home/chung/seqdataQC/NGS2015011E_S1.genome.vcf.gz \
    | gzip -c > /home/chung/seqdataQC/out.vcf.gz
------------------------------------------------------------------------

but I got error as following:

Can't locate Vcf.pm in @INC (@INC contains: /usr/local/lib64/perl5/site_perl /usr/local/lib64/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at vcf-merge line 9.

BEGIN failed--compilation aborted at vcf-merge line 9.

then I find bcftools can also do this, but I have problem installation it,

git clone [--branch=name] git://github.com/samtools/htslib.git htslib
git clone git://github.com/samtools/bcftools.git bcftools
========================================================================

Cloning into 'bcftools'...
fatal: unable to access 'https://github.com/samtools/bcftools.git/': Could not resolve proxy: proxyServer; Unknown error

Please help me solve these problem thank you

[Ram]

Works fine for me. Do you use a proxy server to connect to the Internet?

[chengyi31000]

i have try using this git config --global http.proxy "" but did not work

Answer 1

[aham]

For 'perl vcf-merge' error, the possible reason is export the PATH and PERL5LIB, every time you start using vcftools.
export PERL5LIB=/home/tools/vcftools_0.1.12a/perl
export PATH=$PATH:/home/tools/vcftools_0.1.12a/bin/

[chengyi31000]

I have try again, but it has new error as following how can I deal with it?

sh: tabix: command not found
which: no tabix in (/opt/jdk1.8.0_101/bin:/opt/R-3.3.1/bin/:/opt/plink-1.07-\
x86_64:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/chung/.local/bin:\
/home/chung/bin:/path_to_directory_with_tabix:/home/tools/vcftools_0.1.12a/bin/\
::/home/tools/vcftools_0.1.12a/bin/)

The command "tabix" not found, please add it to your PATH

 at /usr/lib64/perl5/Vcf.pm line 172.
        Vcf::throw('Vcf4_1=HASH(0x19f63b0)', 'The command "tabix" not found, please add it to your PATH\x{a}') called at /usr/lib64/perl5/Vcf.pm line 2672
        VcfReader::get_chromosomes('Vcf4_1=HASH(0x19f63b0)') called at vcf-merge line 197
        main::init_cols('HASH(0x1de2488)', 'Vcf4_2=HASH(0x19f6038)') called at vcf-merge line 279
        main::merge_vcf_files('HASH(0x1de2488)') called at vcf-merge line 12

```

[aham]

While export, have you changed "/home/tools/vcftools_0.1.12a" to your actual path and version of vcftools? I can see in the error it is showing same path as I pasted. Please export with correct path and version of your vcftools. Also you can place/copy the 'tabix' command in '/usr/local/bin/' directory.

[chengyi31000]

when using my path it would have the following error how can I deal with it? [chung@1gIBMgX365073 bin]$ export PERL5LIB= /home/chung/vcftools_0.1.13/perl -bash: export: /home/chung/vcftools_0.1.13/perl': not a valid identifier [chung@1gIBMgX365073 bin]$ export PATH=$PATH: /home/chung/vcftools_0.1.13/bin/ -bash: export:/home/chung/vcftools_0.1.13/bin/': not a valid identifier

[chengyi31000]

WHERE is the "tabix" command ???

[aham]

Sounds like make was not performed after downloading vcftools. Type make and press enter in your vcftools_0.1.13/ directory. After the make, export PATH and PERL5LIB:

export PERL5LIB=/home/chung/vcftools_0.1.13/perl     
export PATH=$PATH:/home/chung/vcftools_0.1.13/bin/

Hopefully it should work.

For tabix, download htslib-1.4 from here. tabix and bgzip are parts of htslib, and these are required for working with vcftools, bcftools.

[chengyi31000]

Thank you ! I will try it.