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Hi,

I use --sample_name option to restrict output reads for PintReads walker (GATK version - 2.4.9).
This option works well but the output BAM header @RG still contains sample name (SM) that was not included.
Is there a way to apply this --sample_name option to BAM header at the same time?
I could reheader the BAM files using samtools but I'm looking for a better and easier way.

Thank you,

Taka

Tagged:

edited March 2014

Hi Geraldine,

Thanks for the reply. I see. Is there a plan to add this function (sample level print reads and reheader at the same time when --sample_name is used) in newer GATK?

Taka

Post edited by tyamaguchi on

I'm not aware of any such plan, sorry.

Geraldine Van der Auwera, PhD

No worries. Thank you for the quick reply!

• Member Posts: 79

Here's +1 for cleaning up the header within PrintReads when using --sample_name. OR add a flag to HC so it can be run when header elements for multiple samples exist... How about adding --sample_name` to HC? Would be even more useful now that I think about it.