GATK: Base quality score recalibration

[fabrice]

Dear experts,

I have used GATK to Base quality score recalibration. After TableRecalibration, it will rewrite the quality scores (in the QUAL field) using the data in the recal_data.csv file, into a new BAM file.

After I got the bam file, should I remapping the bam file using BWA? This is not indicated by GATK. But I just think if we really get more accurate base quality, remapping the reads will be helpful for the mapping also.

Thank you very much.

[swbarnes2]

It's possible that bwa doesn't actually use the base quality when mapping, in which case, reliagnment wouldn't help.

[fabrice]

Why do you think that bwa doesn't actually use the base quality when mapping?