Following the GATK example but the spacing seems off in the command. Is it and how do I correct it? Thanks
Code:
java -jar picard.jar SortSam \ INPUT=/home/cmccabe/IDP/mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.sam \ OUTPUT=/home/cmccabe/Desktop/NGS/picard-tools-1.139/sorted_mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.bam \ SORT_ORDER=coordinate
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