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Is there a way to remove the "|" from the SQ line in a .bam file?
We have several, unique H. pylori genomes. We have aligned each of them to a reference genome, which had "|"in the fasta (or .fa) file name. Now, when running through GATK, we cannot create our final .vcf file. Do we have to remove the "|" from the .fa file and rerun everything from the beginning, or is there another approach?