Multiple Bam Files Into a Single Output File?

[joseph-yclam]

Is there a way to run multiple BAM files in Aldy and have the results from each BAM file contained in a single output file? When I try running each BAM file at a time to the same output file, it overwrites the data from the previous one.

[inumanag]

Hi @joseph-yclam

You can do aldy <bam> -o <bam_output> and then collect all files into a single file. Another way to do this is to use stdout as the output: aldy <bam> -o - >> collected_output. You can also add --simple (recently added) to get a one-line summary of the call (e.g., aldy <bam> --simple -o - >> collected_output).