Isovar on multiple .bam

[JPFinnigan]

Hey,

It would be neat to be able to run isovar on many .bam samples to see how allele-specific expression changes with treatments/time. The specific use-case I have in mind is the change in expression of variant containing transcripts in a cell line with a known genotype in response to exposure to some stimulus.

At present the I'm running isovar on each sample individually, and then cobbling together a table from the results.

[iskandr]

@julia326 and I just ran into needing to pool multiple BAM files together from a single sample. What's the best interface for distinguishing between "one BAM per sample" vs. "many BAMs, single sample"?

One idea is to have --bam A.bam --bam B.bam --rna-multiple-samples vs. --bam A.bam --bam B.bam --rna-combine-alignment-files. What do you think?