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How To Run Vcftools (Simple Question)???

Hello,

After download vfctools, I did the next step:

 /my_path/vcftools_0.1.6 $ make

make[1]: Entering directory `/my_path/vcftools_0.1.6/cpp'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/my_path/vcftools_0.1.6/cpp'
make[1]: Entering directory `/my_path/vcftools_0.1.6/perl'
make[1]: Leaving directory `/my_path/vcftools_0.1.6/perl'

 my_path/vcftools_0.1.6 $ which vcftools
vcftools: Command not found.

How can I run it? What am I missing?

I will really appreciate any help

vcftools vcf
• 9,588 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by Ivan • Ivan

Run 'sudo make install' after your 'make' command?

• 0 views • link
written by Eric Normandeau Eric Normandeau

I've just checked the sources: there is no "make install" in the Makefile. It just compiles the sources. ( Isn't it Aaron ? )

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

1 answer

Invoke bed tools with the fullpath to bedtools:

$ /your/my_path/vcftools_0.1.6/bin/vcftool

or add the path to your $PATH variable:

$ export PATH=${PATH}:/your/my_path/vcftools_0.1.6/bin
$ vcftool
• 3 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

I don't have the sources in front of me. I suppose the path is ".../bin/vcftools"

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

thanks a lot, I did run it!!!

• 0 views • link
written by Ivan • Ivan

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