Building a FASTA consensus sequence from a single BAM file is straightforward. However, if I had several BAM files representing a number of genomes in a population, and I wanted to build a single consensus of all of these BAM files, would I simply get the consensus of all the reads in all the BAMs for each position?
Also, how are positions where equal numbers of reads support a different base resolved?
Also, how are positions where equal numbers of reads support a different base resolved?
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