for the best practice V4, for the step: 2. Raw reads to analysis-ready reads at phase I, I only have lane-level sample data (each sample in one lane, no sample in multi-lanes), so I only did the Fast: lane-level realignment (at known sites only) and lane-level recalibration, which is
for each lane.bam dedup.bam <- MarkDuplicate(lane.bam) realigned.bam <- realign(dedup.bam) [at only known sites, if possible, otherwise skip] recal.bam <- recal(realigned.bam)
Since I do not have multi-lane samples, I do not have to run Fast + per-sample processing, Better: per-sample realignment with known indels and recalibration, or Best: multi-sample realignment with known sites and recalibration, right? It seems that all of these schemes, Better, Best etc, are only for situation when some samples run at multiple lanes, is my understanding correct?
at the paragraph for Fast + per-sample processing, it mentioned: cross-lane realignment, not sure what it means exactly. if every sample of mine are in a single lane, it does not need, right?