Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

MarkDuplicates

minxiongminxiong missouriMember

Hi,
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?

Thanks,
Min

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