pileup2bam

[RockChalkJayhawk]

Anyone aware of a tool that can convert a pileup file to BAM files.

[maubp]

That doesn't make sense. BAM files (like SAM files) describe where individual reads are placed, whereas a pileup file is a coverage based summary of many reads.

[RockChalkJayhawk]

Yes, but theoretically you can re-create the BAM information from the pileup because all the information is stored in the pileup file. Or am I mistaken?

[Alex Renwick]

Going from pileup to bam is a theoretical possibility, but I doubt anyone has taken the trouble to make it a reality. Even the best you could do would miss out on some information, like pairing. Why do you want to do this?

[RockChalkJayhawk]

The problem is I am using an RNA-Seq workflow that produces a pileup rather than a BAM, so I can't annotate it with GATK.

[maubp]

What kind of workflow? If you are using Galaxy it probably is making a BAM file but hiding it by default - check the hidden entries.

[Alex Renwick]

There must be an easier way to get what you want than resurrecting a bam from pileup. You could look at the files upstream of the pileup and see if they can be translated to bam format, or, on the other hand, go forward to create a vcf (or some other bed/gff file) from the pileup and annotate that.

[Peterlorre]

I find myself in this situation using legacy data (e.g., original sequencing files from an old project were lost but pileups are still available). I wanted to bump this thread to see if anyone has come up with a good solution to this problem- any utilities out there that can convert a pileup to a bam or something like it?

[gringer]

You need to be more specific about the pileup format that is used. A text-based format like the output of 'samtools mpileup' would be easier to convert to SAM than a graphical image, for example. But even given the huge amount of information that could be extracted from 'samtools mpileup', it doesn't store everything. For example, the sequence names are not preserved, and no pairing information is retained.

Any pileup output which is nothing more than coverage values without linking between different bases will not be sufficient for generating a source SAM file.

[Peterlorre]

That's a good point- I'm talking about the text-based format, and the experiment was run single-end so pairing isn't important. It's true that I wouldn't have the original read names, but naively that doesn't seem very important- is there software that actually uses those, beyond for read pairing?

That said, I suppose that I hadn't considered whether the pileup format explicitly maintains the individual bases within reads. I had always assumed that the base calls at each position were ordered readwise, but it occurs to me that this may not be the case.

Anyway, it sounds like a tool to do this conversion probably doesn't exist. Thank you for your input.

[gringer]

mpileup does retain read order information in the per-base coverage, but I'm not aware of any other text-based formats that do... actually, I'm not aware of any other text-based formats that do anything more than coverage alone.