Hello, I am using samtools mpileup and I was wondering what a reference skip is. I got output that showed there were nucleotides that skipped the reference. Then, when I compared the reads to the reference I noticed that they were perfect matches. So what does it mean to be a reference skip? Thank you so much for your time. Sincerely, Sammy
-- Samantha Klasfeld Graduate Student Genomics and Computational Biology University of Pennsylvania Philadelphia, PA 19104
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