Question: What's the difference between generating all possible genotypes from a MSA and extracting a consensus sequence?
gravatar for andreagarcia871
6.7 years ago by
andreagarcia87160 wrote:

I have seen examples of getting a consensus sequence by using software like UGENE or JalView. Now what would be an example output of generating all possible genotyopes from a Multiple Sequence Alignment result?


msa genotypes consensus • 1.8k views
ADD COMMENTlink modified 6.6 years ago by Josh Herr5.7k • written 6.7 years ago by andreagarcia87160
gravatar for madk00k
6.6 years ago by
madk00k350 wrote:

I suppose the answer depends on the data you are working with. For example, one should use specialized genotype callers when working with virus populations. However, in general there are a lot of genotype callers available: GATK, FreeBayes, VcfTools. To use one of these tools one has to provide reference sequence and alignment (in BAM format) or a list of mutations (usually in VCF format).


I would select one sequence from multiple alignment as a reference sequence (this could be the consensus sequence, if no reference is available). Then I would remap the sequences forming the alignment to the selected reference using bwa-sw or bowtie2. The resulting BAM file can be used to generate VCF file for genotyping.  


ADD COMMENTlink written 6.6 years ago by madk00k350
gravatar for Josh Herr
6.6 years ago by
Josh Herr5.7k
University of Nebraska
Josh Herr5.7k wrote:

I guess I am wondering why you would want to do this?  You'll be able to easily identify a majority of genotypes by consensus, but rare variants may be hard to discern from sequencing errors.  

You didn't provide us any information in regards to a research question or rationale for this question, so it's hard to provide some input on this basis.

ADD COMMENTlink written 6.6 years ago by Josh Herr5.7k
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