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  • consensus sequence

    have mapped illumina PE reads to the reference genome using BWA and now, would like to get a consensus sequence of the mapped reads- can samtools be used on the aligned bam file??

  • #2
    See this thread: http://seqanswers.com/forums/showthread.php?t=14565 (and the other thread mentioned in #4 there).

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    • #3
      samtools mpileup -uf /<reference.fasta> <aligned.bam> | bcftools view -bcg - > <intermediate.bcf>

      gave me an error: -bash: syntax error near unexpected token "<

      I was wondering BCFtools are part of samtools, right?- is this the correct comand?

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      • #4
        You don't literally use < > around the file names.

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        • #5
          has anyone tried this command to generate a consensus file

          samtools mpileup -uf reference.fasta sorted_alignment.bam | bcftools view -cg - | vcfutils.pl vcf2fq

          but where should I put the output file name???

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          • #6
            Originally posted by mmmm View Post

            but where should I put the output file name???
            Code:
            $ samtools mpileup -uf reference.fasta sorted_alignment.bam | bcftools view -cg - | vcfutils.pl vcf2fq > output_file_name

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            • #7
              yes- thanks.
              I will ignore the abnormal shapes that appeared after the sequence
              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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