On 26 Aug 2015, at 21:02, Samantha Klasfeld <[email protected]> wrote:
> 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?
A reference skip is a CIGAR "N" operation, which usually represents an intron
(see ยง1.4 of the SAM spec). In mpileup's read base column, '>' and '<'
characters show reads that are skipping that position (i.e., line of mpileup
output). So if you look at these reads as they have been mapped in your BAM
file, you will see that they have CIGAR strings that include N operations in
corresponding positions.
John
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