Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

Best Practice V4

mikemike Posts: 103Member
edited November 2012 in Ask the team


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?



Post edited by Geraldine_VdAuwera on


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