Vcftools: Vcf-Merge How To Run ?

Question

[Deniz]

[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 > merged.vcf.gz

-bash: bgzip: command not found 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 /home/X/vcftools0.1.6/lib/Vcf.pm line 2130. The command "tabix -l 1185Euf.flt.vcf.gz" exited with an error. Is the file tabix indexed?

at /home/X/vcftools0.1.6/lib/Vcf.pm line 169 Vcf::throw('Vcf41=HASH(0x2140720)', 'The command "tabix -l 1185Euf.flt.vcf.gz" exited with an err...') called at /home/dincera/vcftools0.1.6/lib/Vcf.pm line 2131 VcfReader::getchromosomes('Vcf41=HASH(0x2140720)') called at ./vcf-merge line 141 main::initcols('HASH(0x213fb98)', 'Vcf40=HASH(0x21405a0)') called at ./vcf-merge line 221 main::mergevcffiles('HASH(0x213fb98)') called at ./vcf-merge line 12

I changed the path.

User specific environment and startup programs

PATH=$PATH:$HOME/bin

export PATH

export PERL5LIB=/share/bin/perl:$HOME/vcftools0.1.6/lib source ~/.bashprofile

I dont know how to run ?

Answer 1

[Rlong]

It looks like you do not have bgzip or tabix installed. Try this link.

Answer 2

[Suresh]

VCF files needs to be position sorted before they get indexed by Tabix. Were VCF files sorted by their position? If not try sorting by position, then run tabix on bgzipped vcf files. Here are the steps to follow: 1) Position sort vcf files 2) bgzip them 3) index by tabix 4) merge the indexed and bgzipped vcf files.

Answer 3

[Deniz]

[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 | /home/X/tabix-0.2.5/bgzip -c > merged.vcf.gz

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 /home/X/vcftools0.1.6/lib/Vcf.pm line 2130. The command "tabix -l 1185Euf.flt.vcf.gz" exited with an error. Is the file tabix indexed?

at /home/X/vcftools0.1.6/lib/Vcf.pm line 169 Vcf::throw('Vcf41=HASH(0x388c720)', 'The command "tabix -l 1185Euf.flt.vcf.gz" exited with an err...') called at /home/X/vcftools0.1.6/lib/Vcf.pm line 2131 VcfReader::getchromosomes('Vcf41=HASH(0x388c720)') called at ./vcf-merge line 141 main::initcols('HASH(0x388bb98)', 'Vcf40=HASH(0x388c5a0)') called at ./vcf-merge line 221 main::mergevcffiles('HASH(0x388bb98)') called at ./vcf-merge line 12

I had tabix and bgzip. I couldnt figure out the problem.

Answer 4

[Joanne Lim]

I think the problem lies here

Can't exec "tabix": No such file or directory at /home/X/vcftools_0.1.6/lib/Vcf.pm line 2130. The command "tabix -l 1185_Euf.flt.vcf.gz" exited with an error. Is the file tabix indexed?

I tried adding tabix into my path with

export PATH=${PATH}:/your/path/to/tabix-0.2.5

as mentioned here

I manage to get a vcf file.

Cheers, Joanne