Daniel:Notebook/Haplotyping/SISSORPipeline/2014-12-3
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Segmentation Analysis Pipeline (Started 12/2/2014)
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