Hi, I'm comparing multiple pipeline, I found that multiple pipelines using BWA-MEM but with different option, and I don't understand all the meaning of its:
bwa mem -Y
(follow by FixMateInformation of Picard, then MarkDuplicate and so on)
2, From GATK Best Practice - in workshop poster: https://drive.google.com/drive/folders/1Nh73FzKde203gUoxyR9CmTd1EcVDMCI5
bwa mem -M
(follow by merging with an unmapped bam file, then MarkDuplicate and so on)
3, Parabrick: https://www.nvidia.com/en-us/docs/parabricks/germline/
(then MarkDuplicate and so on)
From BWA MEM help option:
-Y use soft clipping for supplementary alignments -M mark shorter split hits as secondary
But I don't know why CCDG use -Y with FixMateInformation (while others don't), and why GATK need the unmapped bam? Also, as the document of bwa mem said that -M is necessary for picard MarkDuplicate, both Parabrick and CCDG don't use that option.
Could someone please explain to me these difference? And which one is the most reliable one?
Thank you very much