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When I follow the GATK protocol,
ran below commands:
bwa mem -R '@RG\tID:group1\tSM:sample1\tPL:illumina\tLB:lib1\tPU:C2U2AACXX' ucsc.hg19.fasta ../Unaligned/Project_DefaultProject/Sample_1/1_R1.fastq ../Unaligned/Project_DefaultProject/Sample_1/1_R2.fastq > sample1.sam
java -jar /data/software/picard/MarkDuplicates.jar INPUT=sample1.s
am OUTPUT=sample1_dedup.bam SO=coordinate
I got some error like "ERROR: Unrecognized option: SO"
Why? how to fix it?