SAM tools pileup produces a consensus sequence in vertical format, which is not terribly useful for traditional sequence analysis. Does anyone know of a command line utility to convert SAM tools pileup format to a simple fasta sequence?
I am aware that SAM tools provides tool to convert pileup to fastq samtools.pl pileup2fq), but fastq to fasta conversion presents its own challenges:
Of course I could write a simple script for this task, but I'm hoping someone has already solved this problem for the community. Apologies in advance if this functionality is available in SAM tools itself.
Many thanks, Casey