I am relatively new to galaxy and have been trying to set up a workflow for variant calling used paired end Illumina data (MiSeq). I aligned the reads using BWA-MEM, but have hit a wall using the Mark Duplicate Reads tool. I’ve repeatedly received the error “Value was put into PairInfoMap more than once”, and I don’t seem to be able to correct the problem.
I did use the –M option (Mark Shorter Split Hits as Secondary). Here are the steps I took:
1) FASTQ Groomer on both Fastq Files
2) BWA-MEM with groomed FASTQ’s (-M)
4) Clean Sam (on .BAM file)
4) Paired read mate fixer
5) MarkDuplicate Reads (Failed)
I ran the analysis on the public galaxy server. Any advice/suggestions would be greatly appreciated.