What's the difference between generating all possible genotypes from a MSA and extracting a consensus sequence?

Question

[andreagarcia871]

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?

Answer 1

[madk00k]

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.

Answer 2

[Josh Herr]

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.