The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
@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?