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Working with input files with Q64 and Q33 (IndelRealigner)
Dear GATK team,
I have two input fasta files from exome-seq. One is coded with Q64 and the other is coded with Q33 quality scores. I want to combine the two input fasta files and run bwa+GATK.
How do I combine them for IndelRealigner? I suppose that IndelRealigner needs all reads from both Q64 and Q33. Can I do IndelRealigner separately and then join them? Will this cause problems?
I have searched for many posts but can't find my answers. Please help me.