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)

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
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