Question: Why Vcftools Commands Not Working?
1
gravatar for bioinfo
7.9 years ago by
bioinfo750
bioinfo750 wrote:

I have installed the latest version of Vcftools. I can see there is VcfStats.pm installed in vcftools perl folder below. But when I run some commands (e.g. vcf-comapre file1.vcf.gz file2.vcf.gz; vcf-validator file1.vcf.gz ...etc) its not working.

~/bin/vcftools_0.1.9/perl$ ls

ChangeLog fill-fs test.t vcf-consensus vcf-indel-stats Vcf.pm vcf-stats vcf-validator FaSlice.pm fill-ref-md5 vcf-annotate vcf-convert vcf-isec vcf-query VcfStats.pm fill-aa Makefile vcf-compare vcf-fix-newlines vcf-merge vcf-shuffle-cols vcf-subset fill-an-ac tab-to-vcf vcf-concat vcf-fix-ploidy vcf-phased-join vcf-sort vcf-to-tab

my command:

vcf-stats GMM_homo.vcf.gz

Error message: Can't locate VcfStats.pm in @INC (@INC contains: /lib/perl /lib/perl/Path /etc/perl /usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/siteperl .) at /usr/local/share/vcftools0.1.9/bin/vcf-stats line 9. BEGIN failed--compilation aborted at /usr/local/share/vcftools_0.1.9/bin/vcf-stats line 9.

perl vcftools snp • 7.8k views
ADD COMMENTlink modified 4.7 years ago by bingnas10 • written 7.9 years ago by bioinfo750

Hi Sukhdeep

I have the same problem, and I did not get the post you mentioned above.

Can I get it please!

Bing

ADD REPLYlink modified 7 months ago by RamRS27k • written 4.7 years ago by bingnas10
1

Hi, The link is functional, try again!

ADD REPLYlink written 4.7 years ago by Sukhdeep Singh10k

Yes it is, Thank you so much Sukhdeep!

Bing

ADD REPLYlink modified 7 months ago by RamRS27k • written 4.7 years ago by bingnas10
2
gravatar for Sukhdeep Singh
7.9 years ago by
Netherlands
Sukhdeep Singh10k wrote:

Looks like problem in the path variable, check this post

ADD COMMENTlink written 7.9 years ago by Sukhdeep Singh10k

now I have fixed it..thanks

ADD REPLYlink written 7.9 years ago by bioinfo750
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 781 users visited in the last hour