Re: [Samtools-help] what is a reference skip?

[John M. <jm...@sa...>]

On 26 Aug 2015, at 21:02, Samantha Klasfeld <sj...@co...> 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 §1.4 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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