Why Vcftools Commands Not Working?
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1
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10.1 years ago
bioinfo ▴ 830

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.

vcftools snp perl • 8.9k views
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Hi Sukhdeep

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

Can I get it please!

Bing

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1
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Hi, The link is functional, try again!

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0
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Yes it is, Thank you so much Sukhdeep!

Bing

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2
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10.1 years ago

Looks like problem in the path variable, check this post

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now I have fixed it..thanks

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