No sample names in bam header when using rna_fq2bam

Healthcare & Life Sciences Parabricks
1

I have encountered an issue when using rna_fq2bam followed by haplotypecaller and then gatk combineGVCFs. ran-fq2bam does not add the sample name to the readgroups by default, so although the seperate GVCF are produced, they lack sample IDs. So, when it gets to the joint calling step the combined VCF files only contains one sample as there were no sepaeate sample IDs to combine.
I think this can be overcome with some combination of
–read-group-sm READ_GROUP_SM

–read-group-lb READ_GROUP_LB

–read-group-pl READ_GROUP_PL

–read-group-id-prefix READ_GROUP_ID_PREFIX

is there a worked example of this? If not I will put mine on here.

The cpu equivalent line using STAR where the sample name is $name is
–outSAMattrRGline ID:$name SM:$name

2

Hi @naomi.dyer, thank you for sharing this. I just checked the documentation and we do not have a working example of this so far. If you want to share yours here, please feel free and I can see about adding a more explicit section about this in the documentation.