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I was trying to use the CountTerminusEvent walker and put the following in my bash:
java -Xmx4g -jar /Users/jacquelyn/GenomeAnalysisTK.jar -R /Users/jacquelyn/Sequencing/chr1.fa -T CountTerminusEvent -I /Users/jacquelyn/Desktop/10.NA12878/R_2013_06_24_09_51_35_user_NCR-42-Killary10NA12878r_Auto_user_NCR-42-Killary10NA12878r_43.bam -L /Users/jacquelyn/DeepSeqData/IAD33712_Designed.bed -o /Users/jacquelyn/Desktop/10.NA12878TerminusEvent.txt
I kept getting the error that the argument "o" was not defined. When I queried "CountTerminusEvent -h" in my bash to get help, "--out" wasn't even listed as an argument. I feel stupid asking this question, but what am I doing wrong?