I'm new to the Bioinformatics field and am still learning how to use all the tools and such, but I've been stumped on something that I feel should be very easy for about a week.

Basically, I want to compare the reads in a BAM file to a FASTA reference sequence and get the changes. I can easily view them with **samtools tview** but I need to have it in an Excel file for manipulation/concatenation. I can't seem to figure out why **mpileup** won't give me a straight list of what reads are mutated, unless that's the wrong tool for the job. I'm pretty good at programming, so if the solution is something I need to code for myself I could do it but since the formats are different than what I'm used to, it's been a major headache.

Thanks

<img alt="What I'm dealing with" src="http://i.imgur.com/XR3F7xc.png" style="float:left; height:1687px; width:3168px" />
you need to use bcftools to generate a tabular VCF file:

* http://samtools.sourceforge.net/mpileup.shtml (old version)
* http://www.htslib.org/workflow/#mapping_to_variant (new version)

PS: no, you don't want to have it in an Excel file

PS2: no, you really don't want to have it in an Excel file

PS3: Every time you want to have it in an Excel file, God kills a kitten

PS4:

<img src="https://i.ibb.co/9qnB04y/image.png" width=500 />