Test-drive the GATK tools and Best Practices pipelines on Terra
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Selecting an appropriate quality score
I'm sorry if I'm being dense (I'm new to all this and it is making me feel very dense indeed!), but having read the section on 'Selecting an appropriate quality score threshold' on the 'Best Practice Variant Detection' page, I am still unclear as to whether you mean I should be looking for a QUAL score of at least 30 in a deep coverage data set and should filter out any suggested SNPs that don't meet this, or a GQ score of 30 in each individual sample genotyped at the SNP in question and I only need to filter out individual samples that don't meet this threshold.
Please can you clarify?
I have pasted the bit of text I read below, just to make it clear to which bit I am referring.
A common question is the confidence score threshold to use for variant detection. We recommend:
Deep (> 10x coverage per sample) data: we recommend a minimum confidence score threshold of Q30.
Shallow (< 10x coverage per sample) data: because variants have by necessity lower quality with shallower coverage we recommend a minimum confidence score of Q4 in projects with 100 samples or fewer and Q10 otherwise.