So I am trying to use the the NGS: SAMtools function in galaxy to generate consensus sequences from BAM files that I have for genomic data. I used the generate pileup from BAM dataset tool to generate a pileup and then based on this post https://www.biostars.org/p/1388/#9471 I was trying to generate a consensus sequence in FASTA format. I did the Pileup to Interval step but when I went to do the Extract Genomic DNA step the interval dataset would not show up as an option I could extract Genomic DNA from. It would be really wonderful if someone could let me know what I am doing wrong. I am quite new to this so am not very sure of how each tool works and how the issues can be fixed.
Also does anyone know of a simple way to obtain a consensus sequence from a BAM file in FASTA or FASTQ format? I know most people use SAMtools but I am not well versed with Unix or programming at all so if there is a simpler way that would be very helpful. Please let me know. Thank you!