Daniel:Notebook/Haplotyping/SISSORPipeline/2014-12-3

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Revision as of 22:11, 3 December 2014 by >Djacobse (Created page with "=Segmentation Analysis Pipeline (Started 12/2/2014)= Back to Calendar ...")
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Segmentation Analysis Pipeline (Started 12/2/2014)

Back to Calendar

Reworking the Analysis Pipeline

Looks like there are many steps to rework the pipeline. I'll start at the beginning.

Step 1-Python Script

This doesn't actually need reworking, but I'm having trouble running the command.

Comand

python varbin.50k.sam.py pgp22_chamber1.BQSR.realigned.sam test.varbin50k.txt test.varbin50k.stats.txt

Result

Traceback (most recent call last):
 File "varbin.50k.sam.py", line 129, in <module>
   main()
 File "varbin.50k.sam.py", line 71, in main
   thisRatio = float(binCounts[i]) / (float(counter) / float(len(bins)))
ZeroDivisionError: float division by zero 
awk 'BEGIN {OFS = "\t"} $3 = "chr" $3' pgp22_chamber1.BQSR.realigned.sam > test.sam