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  • sampie
    Member
    • Jun 2014
    • 10
    #1

    How to generate consensus sequence for all refs

    Hi,

    I have been trying to use samtools to create consensus sequences. However, it seems that conseqs.fastq (see command below) is missing consensus sequences for most reference sequences.

    --- samtools command ---
    samtools mpileup -uf ref.fa sorted.bam | bcftools view -cg - | /usr/share/samtools/vcfutils.pl vcf2fq > conseqs.fastq
    ----

    In IGV, I can create consensus sequence for all references (one by one). I would like to create the consensus sequences with a command line tool like samtools. Is there a way to make samtools to produce all consensus sequences like IGV does?

    Thanks
    Tags: None
    • Antony03
      Member
      • Apr 2012
      • 53
      #2
      You should take a look at UGENE. I know this tool can produces consensus with a graphical interface and in command line.

      http://ugene.unipro.ru

        Comment

        • sampie
          Member
          • Jun 2014
          • 10
          #3
          Thanks for reply! UGENE looks like a good tool. However, I was unable to find out how to build consensus sequence with UGENE command line. Can I have an example of a command that can be used to build consensus sequences from ref.fasta and sorted.bam files?

            Comment

            • sampie
              Member
              • Jun 2014
              • 10
              #4
              Hi,

              I tried to isolate a ref sequence and try with that. So, I have ref.fasta with only one sequence. I have also sorted.bam which is an alignment against the ref.fasta. It seems samtools is not working even in case of just one reference.

              Samtools gives an empty mpileup (that is no lines after "#CHROM POS ID..." line) with command: samtools mpileup -uf ref.fasta sorted.bam | bcftools view -cg -

              However, IGV is able to give a consensus sequence (see below). The consensus sequence has only a small sequence (ACGT) portions. Could there be somekind of filtering attached to samtools mpileup, which prevents it from giving the wanted consensus sequence?

              Thanks

              NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCACCAGGGC
              GACGATGCGTAGCCGGCCTGAGAGGGTGGACGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTA
              GGGAATTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAATAAGTATCCCGCCTGGGGAGTACGG
              CCGCAAGGYTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGYATGTGGTTTAATTCGAMGCAACGCGAAGAA
              CCTTACCAGGTCTTGACATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
              Last edited by sampie; 10-07-2014, 05:18 AM.

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