The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
Print Reads --sample_name option doesn't apply to BAM header @RG SM:
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.