Add tags to BAM/SAM file

Question

[dzb]

I'm working with some RNA-seq data. I have alignments done in STAR and the resultant BAM file. I'd like to annotate this BAM alignment data with custom tags using data that are stored in a separate file. The data in the second file contain are a read ID, a barcode, and a UMI. I want to add the barcode and UMI to all reads in the BAM file that match the read ID in the second file.

To summarise:

First file: BAM output from STAR

Second file: Read ID (matching those in STAR BAM file), UMI, barcode.

How do I get the UMI and barcode in file 2 tagged onto the reads in the BAM file?

Intensive Google and forum searching have yielded little info about this but I have a feeling there's a simple answer. Can anyone help?

[GenoMax]

Please post example lines from the two files.

Answer 1

[Matt Shirley]

I don't think there's a simple answer for this question, but if you want to write a script you might find simplesam (https://github.com/mdshw5/simplesam) useful:

[dzb]

This looks like an excellent starting point, thanks for sending it my way.