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.
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?