bam-readcount output: is case significant?

Question

[prograde]

I've noticed that the output for bam-readcount sometimes has bases in uppercase, sometimes lowercase. This is in the reference column, and also for additional columns (after A, C, G, T, N) for indels. Sometimes an indel is even given in mixed case (like "aaaTT").

What is the significance of case in the bam-readcount output?

Answer 1

[prograde]

Answering my own question (I think): the lower case bases originate in my reference FASTA file (soft masked repeats). I re-wrote my reference as all uppercase and the bam-readcount output also became all uppercase (but otherwise the same).

Can anyone confirm or deny that bam-readcount maintains case based on the content of "-f ref.fa"? ...just for the sake of my own sanity.

[Chris Miller]

This is correct. It's looking up the info from your fastq.