Vcftools: Vcf-Merge How To Run ?
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Entering edit mode
10.4 years ago
Deniz ▴ 210

[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 ?

vcftools vcf • 17k views
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4
Entering edit mode
10.4 years ago
Rlong ▴ 340

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

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1
Entering edit mode
10.2 years ago
Suresh ▴ 10

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.

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0
Entering edit mode
10.4 years ago
Deniz ▴ 210

[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.

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Entering edit mode
10.3 years ago
Joanne Lim ▴ 20

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

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