recommended quality control for input BAM files

[sparthib]

Hi, I am just wondering if there is a recommended QC steps that is recommended for input bams?
For e.g. recommended MAPQ threshold for minimap, removing supplementary reads, etc. ?

Thanks,

Sowmya

[andredsim]

Hi Sowmya,

In our pipelines we do not do any extra filtering or QC and use the minimap2 output directly. We do purposely keep supplementary reads in, in the event of fusion genes, however you can remove these if this is not a concern for you. I hope this helps.

Kind Regards,
Andre Sim