allele frequency threshold GATK

[m_elena_bioinfo]

Dear NGS Users,
I have a question about GATK unified genotyper.
How can I set allele frequency threshold in the variant calling?

For example,
Reference sequence T
GATK calls T>C variant with 80count per T e 7count for C.
I would like to set a minor allele frequency of 25% for the calls.
Anyone has any idea?
Thanks a lot

[shoegame2001]

Do you mean remove variants with frequency greater than 25%? I think you can use the SelectVariants tool and include the expression:

--select_expressions "AF>0.25"

[m_elena_bioinfo]

Yes, thank you very much!!
Any advice for the threshold for BaseQRankSum and MQRankSum scores to filter out bad variant called?

Thank u again
ME

[shoegame2001]

Sorry, I am not sure. I am working with a non-model organism, so I do not have a set of validated SNPs to train the program. But if you have such a set that you can download, you can use variant quality score recalibration (http://www.broadinstitute.org/gsa/wi..._recalibration) to calculate VQSLOD, then choose a threshold for that value.

Not sure if you saw this, but I basically followed the directions given here:

http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3