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3.7 years ago
Begonia_pavonina
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150
I am processing VCF files that have been called with FreeBayes version 1.3.1 from target capture data.
I have checked the quality score (QUAL phred-scaled quality score) of the variants on my dataset using bcf stats.
I found out that most of the SNPs are clustered on specific values of QUAL. For example the QUAL values 55, 59, 58. 61, 65 represent more than 30% of the total SNPs on average across samples in the whole dataset.
I have checked if it was related to the average depth of the VCFs withing this range of QUAL, and it is apparently not.
Would anyone know if this clustering around specific values is due to Freebayes, or if it has any biological meaning?
