Interpretation of Genotypic Likelihood in VCF file

[Debanjan_Roy]

Dear all,
I have a small query regarding the quality of Genotype that is reported in a VCF file. In the “PL” field there are 3 numbers for 3 types of genotypic likelihood, which is understandable. However, I have a mutation with all the numbers of the respective genotypic likelihoods to be very low(if I am calculating by 10^(PL/10) formula). Can anyone suggest me whether there is any cutoff number for the “PL” field(among the 3 numbers), which would confirm the respective genotype for the mutation?

Thanks in advance,
Debanjan Roy

[jennaj]

You’ll want to look at more than just the PL field to confirm a genotype. It may help to review the Galaxy variant analysis tutorials:

• https://galaxyproject.github.io/training-material/topics/variant-analysis/
• See the sub-tutorials in this one for more: https://galaxyproject.github.io/training-material/topics/variant-analysis/tutorials/dip/tutorial.html#going-further

Please note that Gemini should be used at Galaxy EU https://usegalaxy.eu and not Galaxy Main https://usegalaxy.org right now. This means that you will need to copy over the example data from one server to another to follow the tutorials. The Gemini tools suite is undergoing an update and is unstable at Galaxy Main. VCFTools and BCFTools are available at both servers.