adding platform information to a bam file

[efoss]

In using "CountCovariates" for base quality score recalibration, I got a complaint that the platform information was missing. I can force it to default to "illumina" with the "-dP" option, but that doesn't seem wise, and I imagine that more problems will crop up in the future if I do that. I looked in the bwa manual to see if there was an option in sampe (like I've seen for adding read group information), but I didn't see anything. Does anyone know how to add this information?

Thank you.

Eric

[sdvie]

Hi Eric,

you have to run AddOrReplaceReadgroups from picard tools for your bams before running the recalibration.

cheers,
Sophia

[efoss]

Hi Eric,

you have to run AddOrReplaceReadgroups from picard tools for your bams before running the recalibration.

cheers,
Sophia

Thanks very much, Sophia. That worked.

Eric