Hello, GATK pipeline recommends perform BQSR for WGS data, which requires read group information added to bam. And this page shows possible values for
PL is ILLUMINA, SOLID, LS454, HELICOS and PACBIO.
My question is which value should
PL be for instruments from BGI such as BGISEQ-500, MGISEQ-T7?
Have you reached out to BGI? Perhaps you could try
GATK. I have not used
GATKin a long time, so not sure if BQSR is still recommended or not?
BQSR is still recommended in the current pipelines but will be retired when the DRAGEN-GATK pipeline comes out later this quarter.