How to Interpret Deletions from varscan?

Question

[amk]

Hi,

We have generated Varscan readcount file from mpileup file generated after alignment. While going through the file at some points we are able to see some deletions like the one below.

Chrom   Position    Reference   Alt
1   11134   G   DEL-1-A

We are wondering how this can happen, as the base present in the reference is G, and the deletion occurred is of A. There are around 17 reads supporting this position. Can some one enlighten us how this notation make sense?

Thanks in advance.

Athul

Answer 1

[shubhra.bhattacharya]

For SNPs and consensus bases, this is the 1-based position of the site or variant. Indels, however, are reported at the base immediately upstream of where they occur. Thus, the first inserted base occurs at (position + 1) and the first deleted base occurs at (position + 1). This is why, for deletions, the reference base (e.g. A) may not match the deleted sequence (e.g. */C)

So basically what you're seeing is +1 base from where the Position is indicated. Hope it clears your doubt!

Source:http://varscan.sourceforge.net/somatic-calling.html

[amk]

Thank you so much Shubhra! It answers the question. :)

Athul