Hey,
this is my current workflow: https://main.g2.bx.psu.edu/u/mj--/w/workflow-whole-exome-somatic-gene-mutati... and the matching *executed* history (with results) https://main.g2.bx.psu.edu/u/mj--/h/workflow-constructed-from-history-httpsc...
My goal is to do 2-3 steps of this pipeline: http://www.nature.com/ng/journal/v44/n6/extref/ng.2256-S1.pdf (page 2) from this paper: http://www.nature.com/ng/journal/v44/n6/pdf/ng.2256.pdf
I have several questions: step 6 in workflow / 22 in history: filter Sam: necessary? If yes, only one flag: "if unmapped: Do not set states?" or the 3 flags I chose? 10/45: realigner: known indels necessary? If yes which ones? (I got this from http://www.broadinstitute.org/gatk//events/2038/GATKwh0-BP-2-Realignment.pdf which says on slide 14 that bam input file is not needed, is that right?) 12/49: BIGGEST PROBLEM: As you can see, the Indel Realigner is empty :( Where is my fault? I did everything the best practices from gatk suggested but it failed anyways.
Any hints, links to papers or answers to fullfil the above mentioned pipeline or to answer my questions are welcome :) Best Moritz