@RG for snp calling on plasmodium knowlesi illumina reads
I am calling snps for the first time, and I am not sure how frame my questions. I am not even sure that GATK is the best method to use. The species is Plasmodium knowlesi. The data are 101nt paired reads sequenced at the Broad. I aligned them to the reference genome using bwa-mem. I am looking over the best practices, but they seem tailored for human data. My questions are 3:
- Is GATK the right tool for me?
- My alignments don't have @RGs. I am aware of the Picard tool AddOrReplaceReadGroups tool (https://broadinstitute.github.io/picard/command-line-overview.html). It requires two inputs for which I don't know what to put. RGLB, and RGPU. Could you please let me know how manage this information?
- What information may I provide to you to help you better address my question?