Question: Generate consensus from BAM file
gravatar for blur
4.2 years ago by
European Union
blur90 wrote:


I wish to get the consensus sequence of a certain section of my bowtie alignment.

I have the bam file, I thought perhaps I need to do faidx - is this possible in Galaxy?



ADD COMMENTlink modified 4.1 years ago by thackl2.6k • written 4.2 years ago by blur90
gravatar for Devon Ryan
4.2 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

I have no idea if someone has made a galaxy pipeline to do this. The general steps are as follows:

  1. Sort and index the BAM file (this can be done with samtools)
  2. Use samtools mpileup like in this post: Questions Regarding Consensus Sequence Calling With Samtools / Bcftools / Vcfutils.Pl Note that I think you can skip the bcftools part step and just give samtools mpileup the -v option.
ADD COMMENTlink written 4.2 years ago by Devon Ryan88k
gravatar for thackl
4.1 years ago by
thackl2.6k wrote:

You can use the bam2cns module of proovread ( It's a consensus based PacBio-Illumina correction software. An advantage might be that the module let's you set a coverage cutoff and it only considers the best alignments (by score) for each location up this cutoff. This is paricularly useful, if you are dealing with repetitive regions, where suboptimal alignments introduce a lot of noise.

ADD COMMENTlink written 4.1 years ago by thackl2.6k
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