bam-readcount -p option

Question

[philip.jonsson]

By reading the documentation I get the impression that the -p switch is for running bam-readcount on multiple libraries in one go, i.e. multiple BAM files. However, I can't really figure out whether I'm supposed to supply a list of files or do something else, and I can't find any example of its usage.

Does anybody have any idea?

[Ram]

Not sure if per library handled multiple BAM files. Could just be multiple libraries from a single BAM file, in which case you might need to merge BAMs

[philip.jonsson]

Ah, of course. That hadn't occurred to me but makes sense.

[Ram]

I'm not sure though - just something that seems plausible given the usage format in the documentation.

Answer 1

[ernfrid]

What RamRS says is true, the program is designed to run on a single BAM file only. The -p flag enables reporting by library for all libraries in a single BAM file. If you have any suggestions on how to make the documentation clearer, please let me know.

[philip.jonsson]

There's just a small window open for misinterpretation, and I happened to look through that window. Not sure any change is needed, but if you were to change anything I guess it would be to more explicitly state that multiple libraries in one BAM file can be analyzed.

[Ram]

<bamfile> usually means a single input. Multiple inputs are usually designated with one mandatory and then a few optional, like so:

<bamfile1> [[bamfile2] [bamfile3] ... [bamfileN]]