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  • Samtools consensus sequence error

    Dear All

    I am again posting this question to the Bioinformatics forum as I didn't get the answer from the Illumina forum.

    I am trying to make consensus sequences using command
    samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq.
    But i am getting this error:

    [bcf_sync] incorrect number of fields (4 != 5) at 15:16294867
    [afs] 0:49470.732 1:50.052 2:33.216

    Can some one help me to sort out this problem. What exactly is going wrong.

    Regards

  • #2
    The issue seems to be in the "bcftools" step in your pipe ie. [bcf_sync].

    Googling suggests two things:

    1. there was an bug in previous bcftools when using "-" stdin, so maybe you have an old bcftools.

    2. this occurs when you have indels, so try the mpileup "-I" option to not call indels and see if the error still occurs.

    Comment


    • #3
      Originally posted by Torst View Post
      The issue seems to be in the "bcftools" step in your pipe ie. [bcf_sync].

      Googling suggests two things:

      1. there was an bug in previous bcftools when using "-" stdin, so maybe you have an old bcftools.

      2. this occurs when you have indels, so try the mpileup "-I" option to not call indels and see if the error still occurs.
      Dear Torst

      Thank you for your reply.

      1. I am using the samtools 0.1.18 version.
      2. I tried what you suggested and I didn't get the error this time but it again stops at the same point and I miss the same no. of chromosomes in the consensus sequence file e.g. when use grep to count the no. of chr in the .fq file I find the few chromosomes missing which was the same with the error also.

      Regards

      Comment

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