Hey,

this is my current workflow:

https://main.g2.bx.psu.edu/u/mj--/w/workflow-whole-exome-somatic-gene-mutation-extraction

and the matching executed history (with results)

https://main.g2.bx.psu.edu/u/mj--/h/workflow-constructed-from-history-httpscreencastg2bxpsueduquickie12illuminapeflowhtml-httpsdocsgooglecomdocumentpubid1zrzrjjocvtau3m-ikl-rbj1f4on60ddliewg7oejdi

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