I have paired end reads of a trio that I eventually need to call variants on (make a .vcf). So I'm experiencing the same thing. Please tell me if my logic is correct:
FASTQ->FASTQC->BWA-MEM (Read group ID assigned as part of this step) -> Sort with SAM Tools -> Filter -> Clean ->Mark Duplicates -> Realign Indels (I think I have to import hg19 or b37 from Shared Data ->Data Libraries -> GATK -> hg19 (import to current history)).
Though I currently have it set to History under reference list, this message still comes up: History does not include a dataset of the required format / build.There is also this section (Binding for reference-ordered data) which I'm not sure what to do with, I'm assuming setting it to indels.
Also, when moving processes forward, should it be the BAM-MEM files only for each step, or the descendent process (i.e. Sorted BAM to filtering rather than the BAM-MEM). Please let me know if you need anymore information to answer my questions. This is a project due soon...