This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Transition and transversion as a quality of SNP call set

Hello,

One of the quality checks for a SNP call set is transition/transversion ratio.

By applying a series of filters, the ratio increases which is said to be an indication of a set with less false positives.

Why with filtering, TS/TV ratio increases?

Thanks!

transition snp
• 2,546 views • link
updated by Santosh Anand Santosh Anand • written by hpapoli hpapoli

Please provide sources to your statements.

• 1 views • link
written by ATpoint ATpoint

1 answer

The whole genome Ts/Tv ratio is around 2.1. If your sample's Ts/Tv deviates significantly from this, most probably there are false positives, and removing them will make the data more close to reality and close to actual Ts/Tv. However, bear in mind that this is an ad-hoc approach and valid (tested) only for human whole genome. Targetted regions and other genomes can have different Ts/Tv ratios. See some interesting discussions here

Ti/Tv Ratio Confirms Snp Discovery. Is This A General Rule?

• 1 views • link
written by Santosh Anand Santosh Anand

Log in to answer this question.

More posts like this