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Old 06-19-2013, 02:01 AM   #1
sadiexiaoyu
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Default bcftools command not found

Hi, All,

I am trying to generate a consensus sequence using samtools. And I used the command as follow:

samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq >cns.fq

But I get the error:

-bash: bcftools: command not found
Use of uninitialized value $l in numeric lt (<) at /Users/samtools-0.1.19/For consensus sequence/vcfutils.pl line 545.
Use of uninitialized value $l in numeric lt (<) at /Users/samtools-0.1.19/For consensus sequence/vcfutils.pl line 545.


I saw bcftools sub-file in samtools file, but there is no bcftools file in the sub-file. Could anyone tell me what is wrong?

Best,

Sadiexiaoyu
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Old 06-19-2013, 03:51 AM   #2
GenoMax
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It appears that the directory containing samtools programs is not in default $PATH.

Have you tried to provide full file system path to the "bcftools" program in the above command?
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Old 06-19-2013, 04:36 AM   #3
sadiexiaoyu
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Quote:
Originally Posted by GenoMax View Post
It appears that the directory containing samtools programs is not in default $PATH.

Have you tried to provide full file system path to the "bcftools" program in the above command?
Hi, GenoMax,

Yes, I tried. I build PATH first to go to samtools directory. And I also tried to build PATH to go to bcftools sub file. But neither worked out...
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Old 06-19-2013, 04:50 AM   #4
GenoMax
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Quote:
Originally Posted by sadiexiaoyu View Post
Hi, GenoMax,

Yes, I tried. I build PATH first to go to samtools directory. And I also tried to build PATH to go to bcftools sub file. But neither worked out...
What version of samtools are you using? What do you mean by sub-file?

Can you post the output of

Code:
$ echo $PATH
and

Code:
$ which samtools
$ which bcftools
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Old 02-16-2014, 01:38 PM   #5
dan
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Seems vcfutils.pl isn't part of samtools / bcftools 19... (it was present in release 18). Has it been wrapped into some other script or options for bcftools itself?

Cheers,
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Old 02-16-2014, 05:17 PM   #6
GenoMax
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vcfutils.pl is in a directory called "bcftools" inside the main samtools directory.
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Old 02-17-2014, 12:47 AM   #7
dan
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Thanks GenoMax, for some reason it's missing in this 'systems' install (bcftools is an exe, not a dir), but I see it when I re-download here:
http://sourceforge.net/projects/samtools/files/

I notice that it's the same file in release 18 and 19.
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