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  • 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

  • #2
    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?

    Comment


    • #3
      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...

      Comment


      • #4
        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

        Comment


        • #5
          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,
          Homepage: Dan Bolser
          MetaBase the database of biological databases.

          Comment


          • #6
            vcfutils.pl is in a directory called "bcftools" inside the main samtools directory.

            Comment


            • #7
              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:
              SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAMtools provide efficient utilities on…


              I notice that it's the same file in release 18 and 19.
              Homepage: Dan Bolser
              MetaBase the database of biological databases.

              Comment

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