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?
If I recall correctly the BGI sequencing technology is close enough to Illumina's that you can use ILLUMINA as PL for BQSR. The PL is just a check to catch certain sequencing types that are so different that the data can't be processed through BQSR.
I have done some researchment. BGISEQ-500 use cPAS(combinatorial probe-anchor synthesis) sequencing which were modified from CG's cPAL sequencing, however I couldn't find details about their cPAS, but I guess it would be similar to ILLUMINA's SBS. MGISEQ-2000 use their new sequencing method called "CoolMPS" which is very different to ILLUMINA's SBS. I think this CoolMPS may don't need to perform BQSR, because their error don't relative to previous base, or to say more randomly.
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version 2.3.6
Have you reached out to BGI? Perhaps you could try
ILLUMINAor contactGATK. I have not usedGATKin 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.