Testing Picard CollectOxoGMetrics and ended up with the following output:
java.lang.NullPointerException.
Adam suggested I submit this.
java -jar picard.jar CollectOxoGMetrics
INPUT=/Users/dkling/Programs/sandbox/firstthree/input/deduppedM.bam
OUTPUT=/Users/dkling/Programs/sandbox/firstthree/expected/CpCGmetricsOpt.bam
REFERENCE_SEQUENCE=/Users/dkling/Programs/sandbox/firstthree/input/ReferenceSequence/human_b37_20.fasta
DB_SNP=/Users/dkling/Programs/sandbox/firstthree/input/dbsnp_138.b37.vcf
I would include the files but the E-mail would be too big.
-David
—
David E. Kling, Ph.D.
Senior Technical Writer
Broad Institute
75 Ames Street, #7003DI
Cambridge, MA 02142
O (617) 714 - 7351
C (617) 291 - 1617
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