I have performed GATK's Base Quality Score Recalibration (BQSR) on my BAM files.
The BQSR has made the per base sequence quality look very bad on FastQC. Is this normal? Should I use the BAM files that have been through BQSR and therefore have worse FastQC reports?
The FastQC per base sequence quality goes from being in the green zone
to being all in the lower red zone
The next step I will do is SNP calling. This is genomic data.
(The BAM files contain only the data that is paired, matches uniquely, and has the duplicates marked by Picard). The FastQC images are from just one of my samples but all samples have the same pattern of being all green or almost all in the green zone, to being entirely in the red zone after BQSR.