What is the relationship between the per-base sequence quality of a FASTQ file and the QUAL of a VCF file

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2.7 years ago

ManuelDB ▴ 110

I have a FASTQ file whose quality is summarised in the following graphs.

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I understand that if a base has a quality score of 30, that means that I have a 99.9% of accuracy that this base has been called correctly. However, when looking at the VCF file generated with the same FASTQ file, I got this

enter image description here

what is the average quality score of the variants called by the different pipelines I have developed. This average QUAL is (according to VCF documentation ) the same Phred-scaled quality score but this time for the assertion made in ALT. So, this really means that accuracy of this bases on average is 100% (because 60 is already 99.9999%)

Is this interpretation correct?

NGS • 387 views

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